I: pbuilder: network access will be disabled during build I: Current time: Sat Jun 3 20:46:53 +14 2023 I: pbuilder-time-stamp: 1685774813 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [openstructure_2.3.1-9.dsc] I: copying [./openstructure_2.3.1.orig.tar.gz] I: copying [./openstructure_2.3.1-9.debian.tar.xz] I: Extracting source gpgv: Signature made Wed May 24 18:59:49 2023 +14 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./openstructure_2.3.1-9.dsc: no acceptable signature found dpkg-source: info: extracting openstructure in openstructure-2.3.1 dpkg-source: info: unpacking openstructure_2.3.1.orig.tar.gz dpkg-source: info: unpacking openstructure_2.3.1-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying python-dist-packages.patch dpkg-source: info: applying fix-quotes-in-ENV.patch dpkg-source: info: applying skip-network-tests.patch dpkg-source: info: applying ost-compare-structures.patch dpkg-source: info: applying ost_config.patch dpkg-source: info: applying skip-dssp-tests.patch dpkg-source: info: applying 86c621b68f23f98fc30ed230be222ce4dd9432cd.patch dpkg-source: info: applying b2798f24c37cb2ff0f46b929a4d41b4f3ce54a68.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 3 20:47 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=3ad4c0b8084c4464855214d8877ecc3e LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1244763 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.B5mJfpLp/pbuilderrc_VzCL --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.B5mJfpLp/b2 --logfile b2/build.log --extrapackages usrmerge openstructure_2.3.1-9.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Jun 3 20:47 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: clustalw, cmake, debhelper-compat (= 13), dh-python, dssp, libboost-all-dev, libeigen3-dev, libfftw3-dev, libglu1-mesa-dev, libopenmm-dev, libopenmm-plugins, libpng-dev, libqt5opengl5-dev, libsqlite3-dev, libtiff-dev, python3-dev, python3-matplotlib, python3-numpy, python3-pil, python3-pyqt5, python3-scipy, qtbase5-dev, sip-dev, voronota dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19591 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on clustalw; however: Package clustalw is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on dssp; however: Package dssp is not installed. pbuilder-satisfydepends-dummy depends on libboost-all-dev; however: Package libboost-all-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libglu1-mesa-dev; however: Package libglu1-mesa-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-dev; however: Package libopenmm-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-plugins; however: Package libopenmm-plugins is not installed. pbuilder-satisfydepends-dummy depends on libpng-dev; however: Package libpng-dev is not installed. pbuilder-satisfydepends-dummy depends on libqt5opengl5-dev; however: Package libqt5opengl5-dev is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on libtiff-dev; however: Package libtiff-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pil; however: Package python3-pil is not installed. pbuilder-satisfydepends-dummy depends on python3-pyqt5; however: Package python3-pyqt5 is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on qtbase5-dev; however: Package qtbase5-dev is not installed. pbuilder-satisfydepends-dummy depends on sip-dev; however: Package sip-dev is not installed. pbuilder-satisfydepends-dummy depends on voronota; however: Package voronota is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} clustalw{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dssp{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lyx{a} gettext{a} gettext-base{a} gfortran-12{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblas3{a} libboost-all-dev{a} libboost-atomic-dev{a} libboost-atomic1.74-dev{a} libboost-atomic1.74.0{a} libboost-chrono-dev{a} libboost-chrono1.74-dev{a} libboost-chrono1.74.0{a} libboost-container-dev{a} libboost-container1.74-dev{a} libboost-container1.74.0{a} libboost-context-dev{a} libboost-context1.74-dev{a} libboost-context1.74.0{a} libboost-coroutine-dev{a} libboost-coroutine1.74-dev{a} libboost-coroutine1.74.0{a} libboost-date-time-dev{a} libboost-date-time1.74-dev{a} libboost-date-time1.74.0{a} libboost-dev{a} libboost-exception-dev{a} libboost-exception1.74-dev{a} libboost-fiber-dev{a} libboost-fiber1.74-dev{a} libboost-fiber1.74.0{a} libboost-filesystem-dev{a} libboost-filesystem1.74-dev{a} libboost-filesystem1.74.0{a} libboost-graph-dev{a} libboost-graph-parallel-dev{a} libboost-graph-parallel1.74-dev{a} libboost-graph-parallel1.74.0{a} libboost-graph1.74-dev{a} libboost-graph1.74.0{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-locale-dev{a} libboost-locale1.74-dev{a} libboost-locale1.74.0{a} libboost-log-dev{a} libboost-log1.74-dev{a} libboost-log1.74.0{a} libboost-math-dev{a} libboost-math1.74-dev{a} libboost-math1.74.0{a} libboost-mpi-dev{a} libboost-mpi-python-dev{a} libboost-mpi-python1.74-dev{a} libboost-mpi-python1.74.0{a} libboost-mpi1.74-dev{a} libboost-mpi1.74.0{a} libboost-nowide-dev{a} libboost-nowide1.74-dev{a} libboost-nowide1.74.0{a} libboost-numpy-dev{a} libboost-numpy1.74-dev{a} libboost-numpy1.74.0{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-python-dev{a} libboost-python1.74-dev{a} libboost-python1.74.0{a} libboost-random-dev{a} libboost-random1.74-dev{a} libboost-random1.74.0{a} libboost-regex-dev{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-serialization-dev{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost-stacktrace-dev{a} libboost-stacktrace1.74-dev{a} libboost-stacktrace1.74.0{a} libboost-system-dev{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost-test-dev{a} libboost-test1.74-dev{a} libboost-test1.74.0{a} libboost-thread-dev{a} libboost-thread1.74-dev{a} libboost-thread1.74.0{a} libboost-timer-dev{a} libboost-timer1.74-dev{a} libboost-timer1.74.0{a} libboost-tools-dev{a} libboost-type-erasure-dev{a} libboost-type-erasure1.74-dev{a} libboost-type-erasure1.74.0{a} libboost-wave-dev{a} libboost-wave1.74-dev{a} libboost-wave1.74.0{a} libboost1.74-dev{a} libboost1.74-tools-dev{a} libbrotli1{a} libbsd0{a} libcbor0.8{a} libcifpp-data{a} libcifpp5{a} libcups2{a} libcurl4{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdouble-conversion3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libegl-dev{a} libegl-mesa0{a} libegl1{a} libeigen3-dev{a} libelf1{a} libevdev2{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-quad3{a} libfftw3-single3{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgbm1{a} libgfortran-12-dev{a} libgfortran5{a} libgl-dev{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglu1-mesa{a} libglu1-mesa-dev{a} libglvnd0{a} libglx-dev{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgudev-1.0-0{a} libharfbuzz0b{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libice6{a} libicu-dev{a} libicu72{a} libimagequant0{a} libinput-bin{a} libinput10{a} libjbig-dev{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp25{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc-dev{a} liblerc4{a} libllvm15{a} libltdl-dev{a} libltdl7{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmd4c0{a} libmtdev1{a} libmunge2{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libopengl-dev{a} libopengl0{a} libopenjp2-7{a} libopenmm-dev{a} libopenmm-plugins{a} libopenmm7.7{a} libopenmpi-dev{a} libopenmpi3{a} libpciaccess0{a} libpcre2-16-0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2{a} libpng-dev{a} libpng16-16{a} libproc2-0{a} libpsl5{a} libpsm-infinipath1{a} libpsm2-2{a} libpthread-stubs0-dev{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libqt5concurrent5{a} libqt5core5a{a} libqt5dbus5{a} libqt5designer5{a} libqt5gui5{a} libqt5help5{a} libqt5network5{a} libqt5opengl5{a} libqt5opengl5-dev{a} libqt5printsupport5{a} libqt5sql5{a} libqt5test5{a} libqt5widgets5{a} libqt5xml5{a} libraqm0{a} librdmacm1{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsm6{a} libsqlite3-dev{a} libssh2-1{a} libsub-override-perl{a} libtcl8.6{a} libtiff-dev{a} libtiff6{a} libtiffxx6{a} libtk8.6{a} libtool{a} libuchardet0{a} libucx0{a} libuv1{a} libvulkan-dev{a} libvulkan1{a} libwacom-common{a} libwacom9{a} libwayland-client0{a} libwayland-server0{a} libwebp-dev{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-icccm4{a} libxcb-image0{a} libxcb-keysyms1{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render-util0{a} libxcb-render0{a} libxcb-shape0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-util1{a} libxcb-xfixes0{a} libxcb-xinerama0{a} libxcb-xinput0{a} libxcb-xkb1{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxfixes3{a} libxft2{a} libxkbcommon-x11-0{a} libxkbcommon0{a} libxml2{a} libxnvctrl0{a} libxrender1{a} libxshmfence1{a} libxsimd-dev{a} libxslt1.1{a} libxss1{a} libxxf86vm1{a} libz3-4{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} mpi-default-bin{a} mpi-default-dev{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-attr{a} python3-beniget{a} python3-brotli{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-fonttools{a} python3-fs{a} python3-gast{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-mpmath{a} python3-numpy{a} python3-packaging{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-ply{a} python3-pyparsing{a} python3-pyqt5{a} python3-pyqt5.sip{a} python3-pythran{a} python3-scipy{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} qt5-qmake{a} qt5-qmake-bin{a} qtbase5-dev{a} qtbase5-dev-tools{a} qtchooser{a} readline-common{a} sensible-utils{a} shared-mime-info{a} sip-dev{a} tk8.6-blt2.5{a} unicode-data{a} voronota{a} x11-common{a} x11proto-dev{a} xkb-data{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus isympy-common javascript-common libarchive-cpio-perl libcoarrays-openmpi-dev libglib2.0-data libldap-common libmail-sendmail-perl libpng-tools libqt5sql5-ibase libqt5sql5-mysql libqt5sql5-odbc libqt5sql5-psql libqt5sql5-sqlite libqt5sql5-tds libqt5svg5 libsasl2-modules lynx mesa-vulkan-drivers psmisc publicsuffix python3-bs4 python3-html5lib python3-olefile python3-sip-dev qt5-gtk-platformtheme qttranslations5-l10n qtwayland5 wget xauth xdg-user-dirs 0 packages upgraded, 432 newly installed, 0 to remove and 0 not upgraded. Need to get 268 MB of archives. After unpacking 1413 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libcbor0.8 amd64 0.8.0-2+b1 [27.4 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libfido2-1 amd64 1.12.0-2+b1 [77.2 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 openssh-client amd64 1:9.2p1-2 [988 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4.1 [593 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 blt amd64 2.5.3+dfsg-4.1 [14.9 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libarchive13 amd64 3.6.2-1 [343 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10 [386 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 librhash0 amd64 1.4.3-3 [134 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 cmake-data all 3.25.1-1 [2026 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 cmake amd64 3.25.1-1 [8692 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74.0 amd64 1.74.0+ds1-21 [487 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libcifpp-data all 5.0.7.1-1 [452 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libcifpp5 amd64 5.0.7.1-1 [802 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 dssp amd64 4.2.2-2 [624 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 fonts-lyx all 2.3.7-1 [186 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libgfortran-12-dev amd64 12.2.0-14 [834 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 gfortran-12 amd64 12.2.0-14 [10.2 MB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libnl-3-200 amd64 3.7.0-0.2+b1 [63.1 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-200 amd64 3.7.0-0.2+b1 [185 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libibverbs1 amd64 44.0-2 [60.7 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 ibverbs-providers amd64 44.0-2 [335 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 icu-devtools amd64 72.1-3 [206 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.6-1 [200 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-tools-dev amd64 1.74.0+ds1-21 [1428 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libboost-tools-dev amd64 1.74.0.3 [4508 B] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libboost-atomic1.74.0 amd64 1.74.0+ds1-21 [220 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libboost-atomic1.74-dev amd64 1.74.0+ds1-21 [221 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libboost-atomic-dev amd64 1.74.0.3 [4640 B] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libboost-chrono1.74.0 amd64 1.74.0+ds1-21 [228 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libboost-chrono1.74-dev amd64 1.74.0+ds1-21 [235 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libboost-chrono-dev amd64 1.74.0.3 [4960 B] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libboost-container1.74.0 amd64 1.74.0+ds1-21 [246 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libboost-container1.74-dev amd64 1.74.0+ds1-21 [250 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libboost-container-dev amd64 1.74.0.3 [4812 B] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libboost-date-time1.74.0 amd64 1.74.0+ds1-21 [217 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libboost-serialization1.74.0 amd64 1.74.0+ds1-21 [317 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libboost-serialization1.74-dev amd64 1.74.0+ds1-21 [359 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libboost-date-time1.74-dev amd64 1.74.0+ds1-21 [226 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libboost-system1.74.0 amd64 1.74.0+ds1-21 [218 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libboost-system1.74-dev amd64 1.74.0+ds1-21 [219 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libboost-thread1.74.0 amd64 1.74.0+ds1-21 [257 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libboost-thread1.74-dev amd64 1.74.0+ds1-21 [267 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libboost-context1.74.0 amd64 1.74.0+ds1-21 [219 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libboost-context1.74-dev amd64 1.74.0+ds1-21 [220 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libboost-context-dev amd64 1.74.0.3 [4540 B] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libboost-coroutine1.74.0 amd64 1.74.0+ds1-21 [234 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libboost-coroutine1.74-dev amd64 1.74.0+ds1-21 [241 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libboost-coroutine-dev amd64 1.74.0.3 [4608 B] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libboost-date-time-dev amd64 1.74.0.3 [4332 B] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libboost-exception1.74-dev amd64 1.74.0+ds1-21 [217 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libboost-exception-dev amd64 1.74.0.3 [4320 B] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem1.74.0 amd64 1.74.0+ds1-21 [258 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem1.74-dev amd64 1.74.0+ds1-21 [279 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 libboost-fiber1.74.0 amd64 1.74.0+ds1-21 [240 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libboost-fiber1.74-dev amd64 1.74.0+ds1-21 [251 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 libboost-fiber-dev amd64 1.74.0.3 [4764 B] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem-dev amd64 1.74.0.3 [4368 B] Get: 142 http://deb.debian.org/debian bookworm/main amd64 libboost-graph1.74.0 amd64 1.74.0+ds1-21 [301 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 libicu-dev amd64 72.1-3 [10.3 MB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74-dev amd64 1.74.0+ds1-21 [557 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 libboost-test1.74.0 amd64 1.74.0+ds1-21 [453 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 libboost-test1.74-dev amd64 1.74.0+ds1-21 [526 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 libboost-graph1.74-dev amd64 1.74.0+ds1-21 [1480 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 libboost-graph-dev amd64 1.74.0.3 [4436 B] Get: 149 http://deb.debian.org/debian bookworm/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-8 [131 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-8 [53.6 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [168 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 librdmacm1 amd64 44.0-2 [68.6 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get: 157 http://deb.debian.org/debian bookworm/main amd64 libmunge2 amd64 0.5.15-2 [19.5 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 libxnvctrl0 amd64 525.85.05-1 [13.3 kB] Get: 160 http://deb.debian.org/debian bookworm/main amd64 ocl-icd-libopencl1 amd64 2.3.1-1 [43.0 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 libhwloc-plugins amd64 2.9.0-1 [17.5 kB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 libpmix2 amd64 4.2.2-1+b1 [622 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 libucx0 amd64 1.13.1-1 [860 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 libopenmpi3 amd64 4.1.4-3+b1 [2422 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 libboost-mpi1.74.0 amd64 1.74.0+ds1-21 [258 kB] Get: 166 http://deb.debian.org/debian bookworm/main amd64 libboost-graph-parallel1.74.0 amd64 1.74.0+ds1-21 [266 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 libboost-graph-parallel1.74-dev amd64 1.74.0+ds1-21 [271 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 libboost-graph-parallel-dev amd64 1.74.0.3 [4460 B] Get: 169 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams1.74-dev amd64 1.74.0+ds1-21 [248 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams-dev amd64 1.74.0.3 [4316 B] Get: 171 http://deb.debian.org/debian bookworm/main amd64 libboost-locale1.74.0 amd64 1.74.0+ds1-21 [449 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 libboost-locale1.74-dev amd64 1.74.0+ds1-21 [551 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 libboost-locale-dev amd64 1.74.0.3 [4660 B] Get: 174 http://deb.debian.org/debian bookworm/main amd64 libboost-log1.74.0 amd64 1.74.0+ds1-21 [599 kB] Get: 175 http://deb.debian.org/debian bookworm/main amd64 libboost-log1.74-dev amd64 1.74.0+ds1-21 [784 kB] Get: 176 http://deb.debian.org/debian bookworm/main amd64 libboost-log-dev amd64 1.74.0.3 [4540 B] Get: 177 http://deb.debian.org/debian bookworm/main amd64 libboost-math1.74.0 amd64 1.74.0+ds1-21 [490 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 libboost-math1.74-dev amd64 1.74.0+ds1-21 [564 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 libboost-math-dev amd64 1.74.0.3 [4532 B] Get: 180 http://deb.debian.org/debian bookworm/main amd64 openmpi-common all 4.1.4-3 [167 kB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 libnl-3-dev amd64 3.7.0-0.2+b1 [104 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-dev amd64 3.7.0-0.2+b1 [203 kB] Get: 183 http://deb.debian.org/debian bookworm/main amd64 libibverbs-dev amd64 44.0-2 [633 kB] Get: 184 http://deb.debian.org/debian bookworm/main amd64 libnuma-dev amd64 2.0.16-1 [35.0 kB] Get: 185 http://deb.debian.org/debian bookworm/main amd64 libltdl7 amd64 2.4.7-5 [393 kB] Get: 186 http://deb.debian.org/debian bookworm/main amd64 libltdl-dev amd64 2.4.7-5 [164 kB] Get: 187 http://deb.debian.org/debian bookworm/main amd64 libhwloc-dev amd64 2.9.0-1 [241 kB] Get: 188 http://deb.debian.org/debian bookworm/main amd64 libevent-2.1-7 amd64 2.1.12-stable-8 [180 kB] Get: 189 http://deb.debian.org/debian bookworm/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-8 [107 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-8 [60.6 kB] Get: 191 http://deb.debian.org/debian bookworm/main amd64 libevent-dev amd64 2.1.12-stable-8 [305 kB] Get: 192 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 libpmix-dev amd64 4.2.2-1+b1 [902 kB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 195 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 196 http://deb.debian.org/debian bookworm/main amd64 openmpi-bin amd64 4.1.4-3+b1 [226 kB] Get: 197 http://deb.debian.org/debian bookworm/main amd64 libopenmpi-dev amd64 4.1.4-3+b1 [970 kB] Get: 198 http://deb.debian.org/debian bookworm/main amd64 mpi-default-dev amd64 1.14 [5548 B] Get: 199 http://deb.debian.org/debian bookworm/main amd64 libboost-mpi1.74-dev amd64 1.74.0+ds1-21 [277 kB] Get: 200 http://deb.debian.org/debian bookworm/main amd64 libboost-mpi-dev amd64 1.74.0.3 [4420 B] Get: 201 http://deb.debian.org/debian bookworm/main amd64 libboost-python1.74.0 amd64 1.74.0+ds1-21 [289 kB] Get: 202 http://deb.debian.org/debian bookworm/main amd64 mpi-default-bin amd64 1.14 [4752 B] Get: 203 http://deb.debian.org/debian bookworm/main amd64 libboost-mpi-python1.74.0 amd64 1.74.0+ds1-21 [341 kB] Get: 204 http://deb.debian.org/debian bookworm/main amd64 libboost-mpi-python1.74-dev amd64 1.74.0+ds1-21 [224 kB] Get: 205 http://deb.debian.org/debian bookworm/main amd64 libboost-mpi-python-dev amd64 1.74.0.3 [4456 B] Get: 206 http://deb.debian.org/debian bookworm/main amd64 libboost-numpy1.74.0 amd64 1.74.0+ds1-21 [229 kB] Get: 207 http://deb.debian.org/debian bookworm/main amd64 libboost-numpy1.74-dev amd64 1.74.0+ds1-21 [232 kB] Get: 208 http://deb.debian.org/debian bookworm/main amd64 libboost-numpy-dev amd64 1.74.0.3 [4376 B] Get: 209 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74.0 amd64 1.74.0+ds1-21 [329 kB] Get: 210 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74-dev amd64 1.74.0+ds1-21 [357 kB] Get: 211 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options-dev amd64 1.74.0.3 [4340 B] Get: 212 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB] Get: 213 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 214 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB] Get: 215 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get: 216 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB] Get: 217 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 218 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 219 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get: 220 http://deb.debian.org/debian bookworm/main amd64 libboost-python1.74-dev amd64 1.74.0+ds1-21 [310 kB] Get: 221 http://deb.debian.org/debian bookworm/main amd64 libboost-python-dev amd64 1.74.0.3 [4632 B] Get: 222 http://deb.debian.org/debian bookworm/main amd64 libboost-random1.74.0 amd64 1.74.0+ds1-21 [226 kB] Get: 223 http://deb.debian.org/debian bookworm/main amd64 libboost-random1.74-dev amd64 1.74.0+ds1-21 [229 kB] Get: 224 http://deb.debian.org/debian bookworm/main amd64 libboost-random-dev amd64 1.74.0.3 [4336 B] Get: 225 http://deb.debian.org/debian bookworm/main amd64 libboost-regex-dev amd64 1.74.0.3 [4600 B] Get: 226 http://deb.debian.org/debian bookworm/main amd64 libboost-serialization-dev amd64 1.74.0.3 [4560 B] Get: 227 http://deb.debian.org/debian bookworm/main amd64 libboost-stacktrace1.74.0 amd64 1.74.0+ds1-21 [260 kB] Get: 228 http://deb.debian.org/debian bookworm/main amd64 libboost-stacktrace1.74-dev amd64 1.74.0+ds1-21 [232 kB] Get: 229 http://deb.debian.org/debian bookworm/main amd64 libboost-stacktrace-dev amd64 1.74.0.3 [4328 B] Get: 230 http://deb.debian.org/debian bookworm/main amd64 libboost-system-dev amd64 1.74.0.3 [4468 B] Get: 231 http://deb.debian.org/debian bookworm/main amd64 libboost-test-dev amd64 1.74.0.3 [4368 B] Get: 232 http://deb.debian.org/debian bookworm/main amd64 libboost-thread-dev amd64 1.74.0.3 [4356 B] Get: 233 http://deb.debian.org/debian bookworm/main amd64 libboost-timer1.74.0 amd64 1.74.0+ds1-21 [226 kB] Get: 234 http://deb.debian.org/debian bookworm/main amd64 libboost-timer1.74-dev amd64 1.74.0+ds1-21 [229 kB] Get: 235 http://deb.debian.org/debian bookworm/main amd64 libboost-timer-dev amd64 1.74.0.3 [4456 B] Get: 236 http://deb.debian.org/debian bookworm/main amd64 libboost-type-erasure1.74.0 amd64 1.74.0+ds1-21 [233 kB] Get: 237 http://deb.debian.org/debian bookworm/main amd64 libboost-type-erasure1.74-dev amd64 1.74.0+ds1-21 [236 kB] Get: 238 http://deb.debian.org/debian bookworm/main amd64 libboost-type-erasure-dev amd64 1.74.0.3 [4428 B] Get: 239 http://deb.debian.org/debian bookworm/main amd64 libboost-wave1.74.0 amd64 1.74.0+ds1-21 [418 kB] Get: 240 http://deb.debian.org/debian bookworm/main amd64 libboost-wave1.74-dev amd64 1.74.0+ds1-21 [473 kB] Get: 241 http://deb.debian.org/debian bookworm/main amd64 libboost-wave-dev amd64 1.74.0.3 [4360 B] Get: 242 http://deb.debian.org/debian bookworm/main amd64 libboost-nowide1.74.0 amd64 1.74.0+ds1-21 [219 kB] Get: 243 http://deb.debian.org/debian bookworm/main amd64 libboost-nowide1.74-dev amd64 1.74.0+ds1-21 [220 kB] Get: 244 http://deb.debian.org/debian bookworm/main amd64 libboost-nowide-dev amd64 1.74.0.3 [4392 B] Get: 245 http://deb.debian.org/debian bookworm/main amd64 libboost-all-dev amd64 1.74.0.3 [4680 B] Get: 246 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3 [244 kB] Get: 247 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 248 http://deb.debian.org/debian bookworm/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB] Get: 249 http://deb.debian.org/debian bookworm/main amd64 libdouble-conversion3 amd64 3.2.1-1 [41.5 kB] Get: 250 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get: 251 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get: 252 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get: 253 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get: 254 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get: 255 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get: 256 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get: 257 http://deb.debian.org/debian bookworm/main amd64 libwayland-server0 amd64 1.21.0-1 [35.9 kB] Get: 258 http://deb.debian.org/debian bookworm/main amd64 libgbm1 amd64 22.3.6-1+deb12u1 [38.0 kB] Get: 259 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get: 260 http://deb.debian.org/debian bookworm/main amd64 libwayland-client0 amd64 1.21.0-1 [28.3 kB] Get: 261 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2 [192 kB] Get: 262 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get: 263 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get: 264 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get: 265 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get: 266 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get: 267 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get: 268 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 269 http://deb.debian.org/debian bookworm/main amd64 libegl-mesa0 amd64 22.3.6-1+deb12u1 [114 kB] Get: 270 http://deb.debian.org/debian bookworm/main amd64 libegl1 amd64 1.6.0-1 [33.7 kB] Get: 271 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get: 272 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 273 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get: 274 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 275 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get: 276 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get: 277 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 278 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get: 279 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get: 280 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get: 281 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get: 282 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get: 283 http://deb.debian.org/debian bookworm/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 284 http://deb.debian.org/debian bookworm/main amd64 x11proto-dev all 2022.1-1 [599 kB] Get: 285 http://deb.debian.org/debian bookworm/main amd64 libxau-dev amd64 1:1.0.9-1 [22.9 kB] Get: 286 http://deb.debian.org/debian bookworm/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get: 287 http://deb.debian.org/debian bookworm/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 288 http://deb.debian.org/debian bookworm/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get: 289 http://deb.debian.org/debian bookworm/main amd64 libxcb1-dev amd64 1.15-1 [181 kB] Get: 290 http://deb.debian.org/debian bookworm/main amd64 libx11-dev amd64 2:1.8.4-2 [836 kB] Get: 291 http://deb.debian.org/debian bookworm/main amd64 libglx-dev amd64 1.6.0-1 [15.3 kB] Get: 292 http://deb.debian.org/debian bookworm/main amd64 libgl-dev amd64 1.6.0-1 [100 kB] Get: 293 http://deb.debian.org/debian bookworm/main amd64 libegl-dev amd64 1.6.0-1 [19.1 kB] Get: 294 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 295 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 296 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 297 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Get: 298 http://deb.debian.org/debian bookworm/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 299 http://deb.debian.org/debian bookworm/main amd64 libevdev2 amd64 1.13.0+dfsg-1 [34.0 kB] Get: 300 http://deb.debian.org/debian bookworm/main amd64 libfftw3-double3 amd64 3.3.10-1 [776 kB] Get: 301 http://deb.debian.org/debian bookworm/main amd64 libfftw3-long3 amd64 3.3.10-1 [337 kB] Get: 302 http://deb.debian.org/debian bookworm/main amd64 libfftw3-quad3 amd64 3.3.10-1 [603 kB] Get: 303 http://deb.debian.org/debian bookworm/main amd64 libfftw3-single3 amd64 3.3.10-1 [806 kB] Get: 304 http://deb.debian.org/debian bookworm/main amd64 libfftw3-bin amd64 3.3.10-1 [51.7 kB] Get: 305 http://deb.debian.org/debian bookworm/main amd64 libfftw3-dev amd64 3.3.10-1 [2123 kB] Get: 306 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 307 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 308 http://deb.debian.org/debian bookworm/main amd64 libopengl0 amd64 1.6.0-1 [30.6 kB] Get: 309 http://deb.debian.org/debian bookworm/main amd64 libglu1-mesa amd64 9.0.2-1.1 [178 kB] Get: 310 http://deb.debian.org/debian bookworm/main amd64 libopengl-dev amd64 1.6.0-1 [4936 B] Get: 311 http://deb.debian.org/debian bookworm/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1 [216 kB] Get: 312 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 313 http://deb.debian.org/debian bookworm/main amd64 libgudev-1.0-0 amd64 237-2 [15.1 kB] Get: 314 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 315 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 316 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get: 317 http://deb.debian.org/debian bookworm/main amd64 libwacom-common all 2.6.0-1 [58.4 kB] Get: 318 http://deb.debian.org/debian bookworm/main amd64 libwacom9 amd64 2.6.0-1 [21.5 kB] Get: 319 http://deb.debian.org/debian bookworm/main amd64 libinput-bin amd64 1.22.1-1 [23.2 kB] Get: 320 http://deb.debian.org/debian bookworm/main amd64 libmtdev1 amd64 1.1.6-1 [23.0 kB] Get: 321 http://deb.debian.org/debian bookworm/main amd64 libinput10 amd64 1.22.1-1 [125 kB] Get: 322 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 323 http://deb.debian.org/debian bookworm/main amd64 libjbig-dev amd64 2.1-6.1 [31.0 kB] Get: 324 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 325 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-2 [290 kB] Get: 326 http://deb.debian.org/debian bookworm/main amd64 libjpeg-dev amd64 1:2.1.5-2 [71.8 kB] Get: 327 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get: 328 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 329 http://deb.debian.org/debian bookworm/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB] Get: 330 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 331 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 332 http://deb.debian.org/debian bookworm/main amd64 liblerc-dev amd64 4.0.0+ds-2 [175 kB] Get: 333 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get: 334 http://deb.debian.org/debian bookworm/main amd64 libmd4c0 amd64 0.4.8-1 [44.2 kB] Get: 335 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get: 336 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get: 337 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB] Get: 338 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-2 [189 kB] Get: 339 http://deb.debian.org/debian bookworm/main amd64 libopenmm7.7 amd64 7.7.0+dfsg-9+b1 [856 kB] Get: 340 http://deb.debian.org/debian bookworm/main amd64 libopenmm-dev amd64 7.7.0+dfsg-9+b1 [327 kB] Get: 341 http://deb.debian.org/debian bookworm/main amd64 libopenmm-plugins amd64 7.7.0+dfsg-9+b1 [1059 kB] Get: 342 http://deb.debian.org/debian bookworm/main amd64 libpcre2-16-0 amd64 10.42-1 [245 kB] Get: 343 http://deb.debian.org/debian bookworm/main amd64 libpng-dev amd64 1.6.39-2 [359 kB] Get: 344 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B] Get: 345 http://deb.debian.org/debian bookworm/main amd64 libqhull-r8.0 amd64 2020.2-5 [248 kB] Get: 346 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get: 347 http://deb.debian.org/debian bookworm/main amd64 libqt5core5a amd64 5.15.8+dfsg-11 [1809 kB] Get: 348 http://deb.debian.org/debian bookworm/main amd64 libqt5concurrent5 amd64 5.15.8+dfsg-11 [42.1 kB] Get: 349 http://deb.debian.org/debian bookworm/main amd64 libqt5dbus5 amd64 5.15.8+dfsg-11 [211 kB] Get: 350 http://deb.debian.org/debian bookworm/main amd64 libqt5network5 amd64 5.15.8+dfsg-11 [674 kB] Get: 351 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 352 http://deb.debian.org/debian bookworm/main amd64 libxcb-icccm4 amd64 0.4.1-1.1 [27.4 kB] Get: 353 http://deb.debian.org/debian bookworm/main amd64 libxcb-util1 amd64 0.4.0-1+b1 [23.2 kB] Get: 354 http://deb.debian.org/debian bookworm/main amd64 libxcb-image0 amd64 0.4.0-2 [22.9 kB] Get: 355 http://deb.debian.org/debian bookworm/main amd64 libxcb-keysyms1 amd64 0.4.0-1+b2 [16.4 kB] Get: 356 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 357 http://deb.debian.org/debian bookworm/main amd64 libxcb-render-util0 amd64 0.3.9-1+b1 [18.3 kB] Get: 358 http://deb.debian.org/debian bookworm/main amd64 libxcb-shape0 amd64 1.15-1 [106 kB] Get: 359 http://deb.debian.org/debian bookworm/main amd64 libxcb-xinerama0 amd64 1.15-1 [105 kB] Get: 360 http://deb.debian.org/debian bookworm/main amd64 libxcb-xinput0 amd64 1.15-1 [130 kB] Get: 361 http://deb.debian.org/debian bookworm/main amd64 libxcb-xkb1 amd64 1.15-1 [129 kB] Get: 362 http://deb.debian.org/debian bookworm/main amd64 xkb-data all 2.35.1-1 [764 kB] Get: 363 http://deb.debian.org/debian bookworm/main amd64 libxkbcommon0 amd64 1.5.0-1 [106 kB] Get: 364 http://deb.debian.org/debian bookworm/main amd64 libxkbcommon-x11-0 amd64 1.5.0-1 [15.6 kB] Get: 365 http://deb.debian.org/debian bookworm/main amd64 libqt5gui5 amd64 5.15.8+dfsg-11 [3408 kB] Get: 366 http://deb.debian.org/debian bookworm/main amd64 libqt5widgets5 amd64 5.15.8+dfsg-11 [2383 kB] Get: 367 http://deb.debian.org/debian bookworm/main amd64 libqt5xml5 amd64 5.15.8+dfsg-11 [122 kB] Get: 368 http://deb.debian.org/debian bookworm/main amd64 libqt5designer5 amd64 5.15.8-2 [2748 kB] Get: 369 http://deb.debian.org/debian bookworm/main amd64 libqt5sql5 amd64 5.15.8+dfsg-11 [122 kB] Get: 370 http://deb.debian.org/debian bookworm/main amd64 libqt5help5 amd64 5.15.8-2 [149 kB] Get: 371 http://deb.debian.org/debian bookworm/main amd64 libqt5opengl5 amd64 5.15.8+dfsg-11 [148 kB] Get: 372 http://deb.debian.org/debian bookworm/main amd64 libqt5printsupport5 amd64 5.15.8+dfsg-11 [202 kB] Get: 373 http://deb.debian.org/debian bookworm/main amd64 libqt5test5 amd64 5.15.8+dfsg-11 [146 kB] Get: 374 http://deb.debian.org/debian bookworm/main amd64 libvulkan1 amd64 1.3.239.0-1 [116 kB] Get: 375 http://deb.debian.org/debian bookworm/main amd64 libvulkan-dev amd64 1.3.239.0-1 [1115 kB] Get: 376 http://deb.debian.org/debian bookworm/main amd64 libxext-dev amd64 2:1.3.4-1+b1 [107 kB] Get: 377 http://deb.debian.org/debian bookworm/main amd64 qt5-qmake-bin amd64 5.15.8+dfsg-11 [1023 kB] Get: 378 http://deb.debian.org/debian bookworm/main amd64 qtchooser amd64 66-2 [26.3 kB] Get: 379 http://deb.debian.org/debian bookworm/main amd64 qt5-qmake amd64 5.15.8+dfsg-11 [221 kB] Get: 380 http://deb.debian.org/debian bookworm/main amd64 qtbase5-dev-tools amd64 5.15.8+dfsg-11 [757 kB] Get: 381 http://deb.debian.org/debian bookworm/main amd64 qtbase5-dev amd64 5.15.8+dfsg-11 [1121 kB] Get: 382 http://deb.debian.org/debian bookworm/main amd64 libqt5opengl5-dev amd64 5.15.8+dfsg-11 [49.1 kB] Get: 383 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get: 384 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-dev amd64 3.40.1-2 [1025 kB] Get: 385 http://deb.debian.org/debian bookworm/main amd64 libzstd-dev amd64 1.5.4+dfsg2-5 [354 kB] Get: 386 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2 [285 kB] Get: 387 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.2 [109 kB] Get: 388 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.2 [99.3 kB] Get: 389 http://deb.debian.org/debian bookworm/main amd64 libwebp-dev amd64 1.2.4-0.2 [400 kB] Get: 390 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6 [316 kB] Get: 391 http://deb.debian.org/debian bookworm/main amd64 libtiffxx6 amd64 4.5.0-6 [144 kB] Get: 392 http://deb.debian.org/debian bookworm/main amd64 libtiff-dev amd64 4.5.0-6 [456 kB] Get: 393 http://deb.debian.org/debian bookworm/main amd64 libxsimd-dev amd64 8.1.0-7 [88.8 kB] Get: 394 http://deb.debian.org/debian bookworm/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB] Get: 395 http://deb.debian.org/debian bookworm/main amd64 python-matplotlib-data all 3.6.3-1 [2744 kB] Get: 396 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get: 397 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B] Get: 398 http://deb.debian.org/debian bookworm/main amd64 python3-appdirs all 1.4.4-3 [13.0 kB] Get: 399 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get: 400 http://deb.debian.org/debian bookworm/main amd64 python3-gast all 0.5.2-2 [9364 B] Get: 401 http://deb.debian.org/debian bookworm/main amd64 python3-beniget all 0.4.1-3 [9920 B] Get: 402 http://deb.debian.org/debian bookworm/main amd64 python3-brotli amd64 1.0.9-2+b6 [281 kB] Get: 403 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 404 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get: 405 http://deb.debian.org/debian bookworm/main amd64 python3-contourpy amd64 1.0.7-1+b1 [176 kB] Get: 406 http://deb.debian.org/debian bookworm/main amd64 python3-cycler all 0.11.0-1 [8020 B] Get: 407 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get: 408 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 409 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB] Get: 410 http://deb.debian.org/debian bookworm/main amd64 python3-ply all 3.11-5 [65.8 kB] Get: 411 http://deb.debian.org/debian bookworm/main amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB] Get: 412 http://deb.debian.org/debian bookworm/main amd64 python3-scipy amd64 1.10.1-2 [15.2 MB] Get: 413 http://deb.debian.org/debian bookworm/main amd64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get: 414 http://deb.debian.org/debian bookworm/main amd64 python3-mpmath all 1.2.1-2 [418 kB] Get: 415 http://deb.debian.org/debian bookworm/main amd64 python3-sympy all 1.11.1-1 [4358 kB] Get: 416 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB] Get: 417 http://deb.debian.org/debian bookworm/main amd64 python3-fs all 2.4.16-2 [95.2 kB] Get: 418 http://deb.debian.org/debian bookworm/main amd64 python3-lxml amd64 4.9.2-1+b1 [1194 kB] Get: 419 http://deb.debian.org/debian bookworm/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b2 [25.0 kB] Get: 420 http://deb.debian.org/debian bookworm/main amd64 unicode-data all 15.0.0-1 [7984 kB] Get: 421 http://deb.debian.org/debian bookworm/main amd64 python3-fonttools amd64 4.38.0-1+b1 [1012 kB] Get: 422 http://deb.debian.org/debian bookworm/main amd64 python3-kiwisolver amd64 1.4.4-1+b1 [60.1 kB] Get: 423 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+b1 [472 kB] Get: 424 http://deb.debian.org/debian bookworm/main amd64 python3-tk amd64 3.11.2-3 [98.3 kB] Get: 425 http://deb.debian.org/debian bookworm/main amd64 python3-pil.imagetk amd64 9.4.0-1.1+b1 [74.4 kB] Get: 426 http://deb.debian.org/debian bookworm/main amd64 python3-pyparsing all 3.0.9-1 [138 kB] Get: 427 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get: 428 http://deb.debian.org/debian bookworm/main amd64 python3-matplotlib amd64 3.6.3-1+b1 [6921 kB] Get: 429 http://deb.debian.org/debian bookworm/main amd64 python3-pyqt5.sip amd64 12.11.1-1 [56.4 kB] Get: 430 http://deb.debian.org/debian bookworm/main amd64 python3-pyqt5 amd64 5.15.9+dfsg-1 [2489 kB] Get: 431 http://deb.debian.org/debian bookworm/main amd64 sip-dev amd64 4.19.25+dfsg-5+b1 [253 kB] Get: 432 http://deb.debian.org/debian bookworm/main amd64 voronota amd64 1.22.3149-2 [2057 kB] Fetched 268 MB in 12s (21.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19591 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19907 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20341 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.2-3_amd64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../005-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... 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Setting up libpthread-stubs0-dev:amd64 (0.4-1) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libopenmm-dev (7.7.0+dfsg-9+b1) ... Setting up libpcre2-16-0:amd64 (10.42-1) ... Setting up libopengl0:amd64 (1.6.0-1) ... Setting up libboost-program-options1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up unicode-data (15.0.0-1) ... Setting up libxsimd-dev:amd64 (8.1.0-7) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpkgconf3:amd64 (1.8.1-1) ... Setting up libuv1:amd64 (1.44.2-1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up libboost-test1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up qt5-qmake-bin (5.15.8+dfsg-11) ... Setting up libsqlite3-dev:amd64 (3.40.1-2) ... Setting up libboost-program-options-dev:amd64 (1.74.0.3) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libavahi-common-data:amd64 (0.8-10) ... Setting up libboost-system1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libdbus-1-3:amd64 (1.14.6-1) ... Setting up libfftw3-quad3:amd64 (3.3.10-1) ... Setting up libboost-nowide1.74-dev (1.74.0+ds1-21) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libboost-regex1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up libproc2-0:amd64 (2:4.0.2-3) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libhwloc15:amd64 (2.9.0-1) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libboost-context1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libevent-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libboost-graph1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... Setting up libboost-random1.74.0:amd64 (1.74.0+ds1-21) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:amd64 (1.9.5-4) ... Setting up icu-devtools (72.1-3) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libboost1.74-tools-dev (1.74.0+ds1-21) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libsensors5:amd64 (1:3.6.0-7.1) ... Setting up liblerc-dev:amd64 (4.0.0+ds-2) ... Setting up libltdl7:amd64 (2.4.7-5) ... Setting up libfftw3-double3:amd64 (3.3.10-1) ... Setting up libcifpp-data (5.0.7.1-1) ... Setting up libglapi-mesa:amd64 (22.3.6-1+deb12u1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libmtdev1:amd64 (1.1.6-1) ... Setting up libvulkan1:amd64 (1.3.239.0-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.2.4-0.2) ... Setting up libboost-atomic1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libboost-math1.74.0:amd64 (1.74.0+ds1-21) ... Setting up liblzma-dev:amd64 (5.4.1-0.2) ... Setting up libboost-serialization1.74.0:amd64 (1.74.0+ds1-21) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up libboost-atomic-dev:amd64 (1.74.0.3) ... Setting up libnuma1:amd64 (2.0.16-1) ... Setting up libboost-container1.74.0:amd64 (1.74.0+ds1-21) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:amd64 (2.3.1-1) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up librhash0:amd64 (1.4.3-3) ... Setting up libtiff6:amd64 (4.5.0-6) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libnl-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libpsm2-2 (11.2.185-2) ... Setting up openmpi-common (4.1.4-3) ... Setting up clustalw (2.1+lgpl-7) ... Setting up libmd4c0:amd64 (0.4.8-1) ... Setting up libopenjp2-7:amd64 (2.5.0-2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up cmake-data (3.25.1-1) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up libglu1-mesa:amd64 (9.0.2-1.1) ... Setting up libboost-math1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.2) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libboost-filesystem1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libopengl-dev:amd64 (1.6.0-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libboost-date-time1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libfido2-1:amd64 (1.12.0-2+b1) ... Setting up libboost-python1.74.0 (1.74.0+ds1-21) ... Setting up libboost-fiber1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libboost-stacktrace1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libboost-test1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up libwebpmux3:amd64 (1.2.4-0.2) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libtiffxx6:amd64 (4.5.0-6) ... Setting up libdeflate-dev:amd64 (1.14-1) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libevdev2:amd64 (1.13.0+dfsg-1) ... Setting up readline-common (8.2-1.3) ... Setting up libboost-timer1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libicu-dev:amd64 (72.1-3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up libboost-filesystem-dev:amd64 (1.74.0.3) ... Setting up libgudev-1.0-0:amd64 (237-2) ... Setting up qtchooser (66-2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libboost-thread1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libboost-numpy1.74.0 (1.74.0+ds1-21) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libwacom-common (2.6.0-1) ... Setting up libxkbcommon0:amd64 (1.5.0-1) ... Setting up libwayland-client0:amd64 (1.21.0-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2022.1-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libboost-log1.74.0 (1.74.0+ds1-21) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:amd64 (2.1.12-stable-8) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up libxau-dev:amd64 (1:1.0.9-1) ... Setting up qt5-qmake:amd64 (5.15.8+dfsg-11) ... Setting up libxcb-xinput0:amd64 (1.15-1) ... Setting up libtool (2.4.7-5) ... Setting up libboost-container1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libarchive13:amd64 (3.6.2-1) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up libboost-chrono-dev:amd64 (1.74.0.3) ... Setting up libfftw3-bin (3.3.10-1) ... Setting up libwacom9:amd64 (2.6.0-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libboost-math-dev:amd64 (1.74.0.3) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libboost-coroutine1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libwebpdemux2:amd64 (1.2.4-0.2) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libboost-system-dev:amd64 (1.74.0.3) ... Setting up libpng-dev:amd64 (1.6.39-2) ... Setting up libxcb-keysyms1:amd64 (0.4.0-1+b2) ... Setting up libxcb-shape0:amd64 (1.15-1) ... Setting up libavahi-common3:amd64 (0.8-10) ... Setting up libjpeg-dev:amd64 (1:2.1.5-2) ... Setting up libjbig-dev:amd64 (2.1-6.1) ... Setting up libevent-openssl-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libxcb-render-util0:amd64 (0.3.9-1+b1) ... Setting up libboost-tools-dev (1.74.0.3) ... Setting up libgfortran-12-dev:amd64 (12.2.0-14) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libxcb-icccm4:amd64 (0.4.1-1.1) ... Setting up libboost-nowide-dev (1.74.0.3) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libboost-container-dev:amd64 (1.74.0.3) ... Setting up libxcb-util1:amd64 (0.4.0-1+b1) ... Setting up pkgconf:amd64 (1.8.1-1) ... Setting up libinput-bin (1.22.1-1) ... Setting up libxcb-xkb1:amd64 (1.15-1) ... Setting up libxcb-image0:amd64 (0.4.0-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.16-1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libboost-test-dev:amd64 (1.74.0.3) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up libcifpp5:amd64 (5.0.7.1-1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.4.7-5) ... Setting up libxdmcp-dev:amd64 (1:1.1.2-3) ... Setting up gfortran-12 (12.2.0-14) ... Setting up libwebp-dev:amd64 (1.2.4-0.2) ... Setting up libxcb-xinerama0:amd64 (1.15-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libtiff-dev:amd64 (4.5.0-6) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up shared-mime-info (2.2-1) ... Setting up libxkbcommon-x11-0:amd64 (1.5.0-1) ... Setting up libevent-dev (2.1.12-stable-8) ... Setting up libboost-random1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libeigen3-dev (3.4.0-4) ... Setting up libboost-timer1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libboost-numpy1.74-dev (1.74.0+ds1-21) ... Setting up pkg-config:amd64 (1.8.1-1) ... Setting up libqt5core5a:amd64 (5.15.8+dfsg-11) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up libboost-serialization1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libopenmm-plugins (7.7.0+dfsg-9+b1) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libboost-wave1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libdrm2:amd64 (2.4.114-1+b1) ... Setting up dwz (0.15-1) ... Setting up libboost-regex1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libnl-3-dev:amd64 (3.7.0-0.2+b1) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up groff-base (1.22.4-10) ... Setting up libqt5dbus5:amd64 (5.15.8+dfsg-11) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libboost-stacktrace-dev:amd64 (1.74.0.3) ... Setting up libllvm15:amd64 (1:15.0.6-4+b1) ... Setting up libxslt1.1:amd64 (1.1.35-1) ... Setting up libcurl4:amd64 (7.88.1-10) ... Setting up libx11-6:amd64 (2:1.8.4-2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libhwloc-dev:amd64 (2.9.0-1) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libboost-locale1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libqt5test5:amd64 (5.15.8+dfsg-11) ... Setting up libboost-regex-dev:amd64 (1.74.0.3) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libfftw3-dev:amd64 (3.3.10-1) ... Setting up libqt5concurrent5:amd64 (5.15.8+dfsg-11) ... Setting up libavahi-client3:amd64 (0.8-10) ... Setting up libboost-timer-dev:amd64 (1.74.0.3) ... Setting up libboost-type-erasure1.74.0:amd64 (1.74.0+ds1-21) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up libinput10:amd64 (1.22.1-1) ... Setting up libx11-xcb1:amd64 (2:1.8.4-2) ... Setting up libibverbs1:amd64 (44.0-2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up libxcb1-dev:amd64 (1.15-1) ... Setting up libboost-wave1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libgbm1:amd64 (22.3.6-1+deb12u1) ... Setting up ibverbs-providers:amd64 (44.0-2) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Setting up libx11-dev:amd64 (2:1.8.4-2) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libboost-random-dev:amd64 (1.74.0.3) ... Setting up libboost-wave-dev:amd64 (1.74.0.3) ... Setting up dssp (4.2.2-2) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libqt5network5:amd64 (5.15.8+dfsg-11) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libxnvctrl0:amd64 (525.85.05-1) ... Setting up libqt5sql5:amd64 (5.15.8+dfsg-11) ... Setting up libboost-iostreams1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libnl-route-3-dev:amd64 (3.7.0-0.2+b1) ... Setting up libboost-date-time1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up qtbase5-dev-tools (5.15.8+dfsg-11) ... Setting up libopenblas-dev:amd64 (0.3.21+ds-4) ... Setting up libqt5xml5:amd64 (5.15.8+dfsg-11) ... Setting up libegl-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libxfixes3:amd64 (1:6.0.0-2) ... Setting up libboost-graph1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up libboost-numpy-dev (1.74.0.3) ... Setting up libboost-serialization-dev:amd64 (1.74.0.3) ... Setting up libboost-date-time-dev:amd64 (1.74.0.3) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b1) ... Setting up libcups2:amd64 (2.4.2-3) ... Setting up libegl1:amd64 (1.6.0-1) ... Setting up cmake (3.25.1-1) ... Setting up libboost-thread1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libboost-thread-dev:amd64 (1.74.0.3) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up librdmacm1:amd64 (44.0-2) ... Setting up libboost-graph-dev:amd64 (1.74.0.3) ... Setting up python3.11 (3.11.2-6) ... Setting up libucx0:amd64 (1.13.1-1) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libboost-log1.74-dev (1.74.0+ds1-21) ... Setting up libpython3.11:amd64 (3.11.2-6) ... Setting up libglx0:amd64 (1.6.0-1) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libboost-iostreams-dev:amd64 (1.74.0.3) ... Setting up libibverbs-dev:amd64 (44.0-2) ... Setting up libhwloc-plugins:amd64 (2.9.0-1) ... Setting up libboost-context1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up python3-tz (2022.7.1-4) ... Setting up python3-six (1.16.0-4) ... Setting up libboost-fiber1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-packaging (23.0-1) ... Setting up libgl1:amd64 (1.6.0-1) ... Setting up libboost-type-erasure1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up libpython3.11-dev:amd64 (3.11.2-6) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up libboost-locale1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up python3-pyqt5.sip (12.11.1-1) ... Setting up python3-lxml:amd64 (4.9.2-1+b1) ... Setting up libglx-dev:amd64 (1.6.0-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up libboost-coroutine1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libboost-coroutine-dev:amd64 (1.74.0.3) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-appdirs (1.4.4-3) ... Setting up libboost-log-dev (1.74.0.3) ... Setting up libgl-dev:amd64 (1.6.0-1) ... Setting up libboost-fiber-dev:amd64 (1.74.0.3) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130) ... Setting up libfabric1:amd64 (1.17.0-3) ... Setting up python3-sympy (1.11.1-1) ... Setting up python3-attr (22.2.0-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up libvulkan-dev:amd64 (1.3.239.0-1) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up libegl-dev:amd64 (1.6.0-1) ... Setting up libpmix2:amd64 (4.2.2-1+b1) ... Setting up python3-lz4 (4.0.2+dfsg-1+b2) ... Setting up python3.11-dev (3.11.2-6) ... Setting up libopenmpi3:amd64 (4.1.4-3+b1) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up python3-ply (3.11-5) ... Setting up libboost-mpi1.74.0 (1.74.0+ds1-21) ... Setting up libqt5gui5:amd64 (5.15.8+dfsg-11) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-tk:amd64 (3.11.2-3) ... Setting up libboost-locale-dev:amd64 (1.74.0.3) ... Setting up libqt5widgets5:amd64 (5.15.8+dfsg-11) ... Setting up libboost-context-dev:amd64 (1.74.0.3) ... Setting up libqt5help5:amd64 (5.15.8-2) ... Setting up libboost-type-erasure-dev:amd64 (1.74.0.3) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up libqt5printsupport5:amd64 (5.15.8+dfsg-11) ... Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up libglu1-mesa-dev:amd64 (9.0.2-1.1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up qtbase5-dev:amd64 (5.15.8+dfsg-11) ... Setting up libqt5opengl5:amd64 (5.15.8+dfsg-11) ... Setting up python3-contourpy (1.0.7-1+b1) ... Setting up libboost-graph-parallel1.74.0 (1.74.0+ds1-21) ... Setting up libpmix-dev:amd64 (4.2.2-1+b1) ... Setting up openmpi-bin (4.1.4-3+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up python3-all-dev (3.11.2-1+b1) ... Setting up libqt5designer5:amd64 (5.15.8-2) ... Setting up libqt5opengl5-dev:amd64 (5.15.8+dfsg-11) ... Setting up mpi-default-bin (1.14) ... Setting up libboost-python1.74-dev (1.74.0+ds1-21) ... Setting up libboost-python-dev (1.74.0.3) ... Setting up libboost-graph-parallel1.74-dev (1.74.0+ds1-21) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up libopenmpi-dev:amd64 (4.1.4-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up python3-pyqt5 (5.15.9+dfsg-1) ... Setting up libboost-mpi-python1.74.0 (1.74.0+ds1-21) ... Setting up python3-scipy (1.10.1-2) ... Setting up libboost-graph-parallel-dev (1.74.0.3) ... Setting up mpi-default-dev (1.14) ... Setting up libboost-mpi1.74-dev (1.74.0+ds1-21) ... Setting up libboost-mpi-python1.74-dev (1.74.0+ds1-21) ... Setting up libboost-mpi-python-dev (1.74.0.3) ... Setting up libboost-mpi-dev (1.74.0.3) ... Setting up libboost-all-dev (1.74.0.3) ... Setting up python3-fonttools (4.38.0-1+b1) ... Setting up python3-pil:amd64 (9.4.0-1.1+b1) ... Setting up python3-pil.imagetk:amd64 (9.4.0-1.1+b1) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-1+b1) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/openstructure-2.3.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../openstructure_2.3.1-9_source.changes dpkg-buildpackage: info: source package openstructure dpkg-buildpackage: info: source version 2.3.1-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/openstructure-2.3.1' dh_auto_configure -- -DOPTIMIZE=ON -DUBUNTU_LAYOUT=ON -DENABLE_MM=ON -DOPEN_MM_PLUGIN_DIR=/usr/lib/x86_64-linux-gnu/openmm/plugins cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DOPTIMIZE=ON -DUBUNTU_LAYOUT=ON -DENABLE_MM=ON -DOPEN_MM_PLUGIN_DIR=/usr/lib/x86_64-linux-gnu/openmm/plugins .. -- The CXX compiler identification is GNU 12.2.0 -- The C compiler identification is GNU 12.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of void* -- Check size of void* - done -- Found Python: /usr/bin/python3 (found suitable version "3.11.2", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- Found Boost package: python311 -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.31") found components: unit_test_framework -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.31") found components: filesystem system -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.31") found components: iostreams regex -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.31") found components: program_options -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.31") found components: regex -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.31") found components: thread chrono date_time atomic -- Found OpenGL: /usr/lib/x86_64-linux-gnu/libOpenGL.so -- Found EIGEN: /usr/include/eigen3 (Required is at least version "3.2.0") -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so (Required is at least version "3.7.13") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.13") -- Found PNG: /usr/lib/x86_64-linux-gnu/libpng.so (found version "1.6.39") -- Found FFTW: /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Found TIFF: /usr/lib/x86_64-linux-gnu/libtiff.so (found version "4.5.0") -- Found OpenMM: /usr/lib/x86_64-linux-gnu/libOpenMM.so -- Searching for python module PyQt5 for /usr/bin/python3 -- Found python module PyQt5 -- Searching for python module PyQt5.sip for /usr/bin/python3 -- Found python module PyQt5.sip -- OpenStructure will be built with the following options: Install Prefix (-DPREFIX) : /usr RPath in install (-DUSE_RPATH) : OFF Info support (-DENABLE_INFO) : ON Graphical interface (-DENABLE_GUI) : ON OpenGL support (-DENABLE_GFX) : ON Shader support (-DUSE_SHADER) : OFF Numpy support (-DUSE_NUMPY) : OFF SpaceNav Device support (-DENABLE_SPNAV) : OFF OpenMM support (-DENABLE_MM) : ON OpenMM plugins (-DOPEN_MM_PLUGIN_DIR) : /usr/lib/x86_64-linux-gnu/openmm/plugins Optimize (-DOPTIMIZE) : ON Profiling support (-DPROFILE) : OFF Double Precision (-DUSE_DOUBLE_PRECISION) : OFF Compound Lib (-DCOMPOUND_LIB) : NONE TMAlign and TMScore (-DCOMPILE_TMTOOLS) : OFF Static Libraries (-DENABLE_STATIC) : OFF Debian/Ubuntu directory layout (-DUBUNTU_LAYOUT) : ON Hidden object visibility (-DHIDDEN_VISIBILITY) : OFF -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/openstructure-2.3.1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/openstructure-2.3.1' dh_auto_build cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/openstructure-2.3.1 -B/build/openstructure-2.3.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/openstructure-2.3.1/obj-x86_64-linux-gnu/CMakeFiles /build/openstructure-2.3.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/create_stage.dir/DependInfo.cmake --color= make -f modules/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.py.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/subst___init__.py.dir/DependInfo.cmake --color= make -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/DependInfo.cmake --color= make -f modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build.make modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/DependInfo.cmake --color= make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod/CMakeFiles/ost_db_pymod.dir/DependInfo.cmake --color= make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/DependInfo.cmake --color= make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/DependInfo.cmake --color= make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib make -f modules/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.py.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/modules/base/pymod/__init__.py.in -DOUT_FILE=__init__.py -DALL_ADDITIONAL_MODULES=,\'gui\',\'gfx\',\'img\',\'info\' -P /build/openstructure-2.3.1/cmake_support/substitute.cmake make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/share /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share/CMakeFiles/scene_icons.dir/DependInfo.cmake --color= make -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./__init__.py make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/db/./__init__.py make -f modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build.make modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./__init__.py make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/bin make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/geom/./__init__.py make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./lga.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./lga.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./__init__.py make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/share /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share/CMakeFiles/gui_images.dir/DependInfo.cmake --color= make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/DependInfo.cmake --color= make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/pymod/./cleanup.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./cleanup.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/add_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/add_icon.png cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/pymod/./py_gfx_obj.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./py_gfx_obj.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hbplus.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hbplus.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 0%] Built target subst___init__.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/images/logo-small.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/images/logo-small.png make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/__init__.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/close_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/close_icon.png make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/depend [ 0%] Built target ost_db_pymod [ 0%] Built target ost_geom_pymod make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./msms.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./msms.py make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/DependInfo.cmake --color= make -f modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/__init__.py make -f modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build.make modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/critical_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/critical_icon.png make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/color_options_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_options_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/DependInfo.cmake --color= [ 0%] Built target ost_gfx_pymod [ 0%] Built target ost_conop_pymod make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./tmtools.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./tmtools.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/termuse.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/termuse.py make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./__init__.py make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/color_select_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_select_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/delete_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/delete_icon.png make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/./__init__.py make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/depend [ 0%] Built target gui_images cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./dssp.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dssp.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/ost_info_pymod.dir/DependInfo.cmake --color= make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 0%] Built target create_stage make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod/CMakeFiles/ost_io_pymod.dir/DependInfo.cmake --color= make -f modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build.make modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/alg/./__init__.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/superpositiondialog.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/superpositiondialog.py make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/DependInfo.cmake --color= make -f modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build.make modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./init_context_menu.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_context_menu.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/combo_options_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/combo_options_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/distance_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/distance_icon.png make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/DependInfo.cmake --color= make -f modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build.make modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./clustalw.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./clustalw.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/init.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/init.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/info/./__init__.py make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/cpk_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/cpk_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/find_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/find_icon.png make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./__init__.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./init_menubar.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_menubar.py make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/./__init__.py make -f modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build.make modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./utils.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./utils.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 0%] Built target ost_img_pymod make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./__init__.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./forcefield.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./forcefield.hh make -f modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build.make modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/menu.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/menu.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/information_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/information_icon.png make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./__init__.py make -f modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build.make modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/depend [ 0%] Built target ost_img_alg_pymod make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/DependInfo.cmake --color= make -f modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build.make modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/pymod/./remote.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./remote.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/custom_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/custom_widget.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./init_spacenav.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_spacenav.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/DependInfo.cmake --color= make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./naccess.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./naccess.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_startup.py.dir/DependInfo.cmake --color= make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/map_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/map_icon.png make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_config.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./views.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./views.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./ff_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./ff_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/pymod/./repository.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./repository.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/pymod/./antechamber.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./antechamber.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build.make modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 0%] Built target ost_info_pymod make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_editor_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_editor_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/./__init__.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hhblits.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./init_splash.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_splash.py make -f modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build.make modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/menubar_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/menubar_icon.png [ 0%] Built target ost_mol_pymod make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/./__init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./__init__.py make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./superpose.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./superpose.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost_config.in -DOUT_FILE=ost_config -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake [ 0%] Built target ost_gui_dng_pymod cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./trajectory_viewer.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./trajectory_viewer.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./buildingblock.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./buildingblock.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_info_handler.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_info_handler.py make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/./mat.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./mat.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hhblits2.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits2.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./qsscoring.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./qsscoring.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/rigid_body_manipulator_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/rigid_body_manipulator_icon.png make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./helpwidget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./helpwidget.py [ 0%] Built target ost_mol_mm_pymod [ 0%] Built target ost_seq_pymod make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 0%] Built target ost_io_pymod cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./block_modifiers.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/actions /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/actions /build/openstructure-2.3.1/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_list_model.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_list_model.py make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hhblits3.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits3.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom_headers.dir/DependInfo.cmake --color= make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/./renumber.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./renumber.py [ 0%] Built target subst_ost_startup.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config_headers.dir/DependInfo.cmake --color= make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./trajectory_analysis.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./trajectory_analysis.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/ost_base_headers.dir/DependInfo.cmake --color= make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/selection_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/selection_icon.png cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./table.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./table.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./gromacs_block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./gromacs_block_modifiers.hh make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost.in -DOUT_FILE=ost -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./blast.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./blast.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/actions/ost-compare-structures /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-structures [ 0%] Built target subst_ost_config make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_preset_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_preset_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/ost_base_pymod.dir/DependInfo.cmake --color= make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/show_sidebar_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/show_sidebar_icon.png cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/./aaindex.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./aaindex.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/dng.in -DOUT_FILE=dng -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./structure_analysis.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./structure_analysis.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/DependInfo.cmake --color= make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./gosty_startup.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./gosty_startup.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./cadscore.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./cadscore.py make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/export_helper/vector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/export_helper/vector.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./heuristic_block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./heuristic_block_modifiers.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/hsc_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/hsc_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./base.hh make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/generic_property_def.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/generic_property_def.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/site_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/site_icon.png make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex1 /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex1 make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./helix_kinks.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./helix_kinks.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./kclust.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./kclust.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./settings.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./interaction.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./interaction.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/immutable_gradient_info_handler.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_gradient_info_handler.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/split_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/split_icon.png cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/pair_to_tuple_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./def.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./def.hh [ 0%] Built target subst_ost make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src/CMakeFiles/ost_info_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./stutil.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex2 /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex2 [ 0%] Built target actions cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/warning_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/warning_icon.png cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./dllexport.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./dllexport.hh make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./hbond.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./hbond.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./ialign.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./ialign.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/DependInfo.cmake --color= [ 0%] Built target ost_gui_pymod cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/immutable_preset_info_handler.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_preset_info_handler.py make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/vec_to_list_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/vec_to_list_conv.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./settings.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./settings.hh [ 0%] Built target subst_dng make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/DependInfo.cmake --color= make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./exc.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./exc.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/refresh.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/refresh.png cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./table.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./version.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./version.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex3 /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex3 make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./mmseqs2.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./mmseqs2.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/init_inspector.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/init_inspector.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./table_selector.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./simulation.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./simulation.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/test_utils/compare_files.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/test_utils/compare_files.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./geom.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./geom.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/pointer_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 0%] Built target ost_mol_alg_pymod cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_error.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/src/./wrap_tmalign.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/bindings/./wrap_tmalign.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./modeller.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./modeller.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./xmlrunner.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./generic_property.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./generic_property.hh [ 0%] Built target ost_config_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat.hh [ 0%] Built target scene_icons make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/inspector_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/inspector_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./conop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./conop.hh make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl.hh make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src/CMakeFiles/ost_db_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./observer.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/DependInfo.cmake --color= make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./testutils.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh [ 0%] Built target ost_seq_alg_pymod make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./integrity_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./integrity_error.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake --color= [ 0%] Built target ost_bindings_pymod cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_group.hh make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat2.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/DependInfo.cmake --color= make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./processor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./processor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl_fw.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src/CMakeFiles/ost_io_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/map_level_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/map_level_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./state_extractor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./state_extractor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./invalid_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./invalid_handle.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different __init__.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/__init__.py [ 0%] Built target ost_bindings_headers make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat3.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./alignment_opts.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./alignment_opts.hh make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_handle.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_wrap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./amino_acids.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./amino_acids.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_list.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./system_creator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./system_creator.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./ptr_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./ptr_observer.hh make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./anisotropic.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./anisotropic.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./clip_alignment.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_conv.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat4.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat4.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_group.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/dispatch.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/dispatch.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./conservation.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./conservation.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./diag.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./diag.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology_creator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology_creator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./log.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/remote.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/remote.py [ 0%] Built target ost_base_pymod make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_item.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_item.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/star_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/star_parser.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./auto_correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./svd_superpose.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./svd_superpose.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log_sink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./log_sink.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./model_check.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./model_check.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./alignment_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./alignment_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./linear_indexer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./linear_indexer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_prediction_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./index.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./index.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_list_model.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_list_model.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec2.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_fw.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./clear.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clear.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./profile.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./binary_container.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./binary_container.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./heuristic.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./heuristic.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec3.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./clip_min_max.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./dyn_cast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./dyn_cast.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./steep.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./steep.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./extract_data_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./extract_data_helper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./distance_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./sec_structure_segments.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec4.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec4.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./conjugate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./conjugate.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./stdint.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./stdint.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_info_handler.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_info_handler.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_path.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_path.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/io_profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_region.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_region.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./entropy.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./entropy.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound_lib.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./convolute.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./convolute.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_def.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./stdint_msc.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./stdint_msc.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./local_dist_diff_test.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./local_dist_diff_test.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_set.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_set.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_list_model.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_list_model.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_spec.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh [ 0%] Built target ost_mol_mm_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_column.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column.hh [ 0%] Built target ost_db_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat2_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./correlate.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./range.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./range.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_factory.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./global_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./global_align.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake --color= make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./distance_test_common.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_visitor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_frequency_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat3_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/dihedral.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./rule_based.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./rule_based.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./cross_correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./cross_correlate.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_column_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./ins_del.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./units.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./units.hh make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_verbose_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./distance_rmsd_test.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_rmsd_test.hh make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/render_mode_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_mode_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'modules/config/CMakeFiles/ost_config.dir/build'. make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./minimal_compound_lib.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat4_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./density_slice.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./density_slice.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pqr_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./message.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./message.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./local_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./local_align.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./invalid_sequence.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/render_op.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_op.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_option_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./item_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mae_handler.hh [ 0%] Built target ost_config cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./superpose_frames.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_spatial_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound_lib_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./platform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./platform.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./circular_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./circular_iterator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./dft.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./dft.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./merge_pairwise_alignments.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./views_from_sequences.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/render_options_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_options_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./geom_info_conversion.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./filter_clashes.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./item_type_cast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type_cast.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./string_ref.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./string_ref.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./ring_finder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./ring_finder.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fft.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fft.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./constants.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./constants.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./profile_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./profile_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/scene_observer_impl.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_observer_impl.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_handler.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./pod_vector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./pod_vector.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fftw_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fftw_helper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./construct_cbeta.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh [ 0%] Built target ost_info_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh [ 0%] Built target ost_conop_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/scene_selection_helper.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_selection_helper.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fill.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fill.hh [ 0%] Built target ost_seq_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./fixed_string.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./fixed_string.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./semiglobal_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pdb_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./clash_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/simple_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/simple_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./filter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./filter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/index.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/index.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./tri_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./tri_matrix.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_option.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./sequence_identity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_identity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fourier_filters.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/sline_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/sline_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./trajectory_analysis.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./boost_filesystem_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/type_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_gradient_magnitude.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./structure_analysis.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/toolbar_options_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/toolbar_options_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./paged_array.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./paged_array.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite2_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./sequence_similarity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/value_holder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/value_holder.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/trace_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/trace_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite3_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/manipulator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./algorithm.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./pdbize.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/tube_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/tube_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_laplacian.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh [ 0%] Built target ost_base_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./variance_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./aligned_cuboid.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./adjacency_bitmap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/uniform_color_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/uniform_color_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./circle_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./circle_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./highest_peak_search_3d.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec_mat_predicates.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/save_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/save_entity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/visibility_op.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/visibility_op.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./composite_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./composite_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./histogram.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./histogram.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./quat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./quat.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_entity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/line_trace_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/line_trace_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./contact_overlap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/map_tool.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_algorithm.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./line_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./transform.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_pseudo_counts.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/wireframe_widget.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/wireframe_widget.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./domain_find.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./local_sigma_threshold.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_observer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./point_cloud.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./point_cloud.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/query_editor.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/query_editor.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_surface.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./similarity_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./mask_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./mask_image.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_row.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_types.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_types.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./accessibility.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./accessibility.hh [ 0%] Built target ost_seq_alg_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh [ 0%] Built target ost_gui_scene_pymod cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./negate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./negate.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/tabulated_trig.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./sec_struct.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_struct.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer_factory.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./nonstandard.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./nonstandard.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./debug.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./debug.hh [ 0%] Built target ost_geom_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/painter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./molck.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./molck.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_view.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/omf.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./dllexport.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./dllexport.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/secstr_row.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./find_membrane.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/load_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/load_map.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_iterator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat2.cc.o [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat3.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_secstr_painter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat2.cc.o -MF CMakeFiles/ost_geom.dir/mat2.cc.o.d -o CMakeFiles/ost_geom.dir/mat2.cc.o -c /build/openstructure-2.3.1/modules/geom/src/mat2.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./entity_to_density.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/custom_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/custom_render_options.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat4.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat3.cc.o -MF CMakeFiles/ost_geom.dir/mat3.cc.o.d -o CMakeFiles/ost_geom.dir/mat3.cc.o -c /build/openstructure-2.3.1/modules/geom/src/mat3.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_table.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_table.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vec3.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat4.cc.o -MF CMakeFiles/ost_geom.dir/mat4.cc.o.d -o CMakeFiles/ost_geom.dir/mat4.cc.o -c /build/openstructure-2.3.1/modules/geom/src/mat4.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vec3.cc.o -MF CMakeFiles/ost_geom.dir/vec3.cc.o.d -o CMakeFiles/ost_geom.dir/vec3.cc.o -c /build/openstructure-2.3.1/modules/geom/src/vec3.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat2_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_linear.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_selection_painter.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat3_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat2_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat2_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat2_op.cc.o -c /build/openstructure-2.3.1/modules/geom/src/vecmat2_op.cc make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cpk_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat3_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat3_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat3_op.cc.o -c /build/openstructure-2.3.1/modules/geom/src/vecmat3_op.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/image_format.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/image_format.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_log.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_log.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite2.cc.o -MF CMakeFiles/ost_geom.dir/composite2.cc.o.d -o CMakeFiles/ost_geom.dir/composite2.cc.o -c /build/openstructure-2.3.1/modules/geom/src/composite2.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_text_painter.hh [ 1%] Built target ost_mol_alg_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat4_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat4_op.cc.o -c /build/openstructure-2.3.1/modules/geom/src/vecmat4_op.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_od.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_od.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_factory.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_factory.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/sline_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_view.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite3.cc.o -MF CMakeFiles/ost_geom.dir/composite3.cc.o.d -o CMakeFiles/ost_geom.dir/composite3.cc.o -c /build/openstructure-2.3.1/modules/geom/src/composite3.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./power_spectrum.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_model.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_trace_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_type.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./randomize.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./randomize.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_row.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_class.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_class.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cartoon_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./smooth_mask_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/trace_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_type.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_table_view.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_group.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_list.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_accumulator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_source.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_min_max.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./in_mem_coord_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./in_mem_coord_source.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/tick_painter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./threshold.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./threshold.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_frame.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_frame.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/title_row.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transcendentals.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/alignment_view_object.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./inverted_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./inverted_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_view_object.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./map.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transform_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_view_object.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/basic_gradient_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/main_thread_runner.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_transform.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./mol.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./mol.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/tiff_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_mirror.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_mirror.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/completer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/completer_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_shift.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/jpk_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/jpk_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_pass.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_pass.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_visitor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./discrete_shrink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./bitmap_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/gutter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformation_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./collada_exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/path_completer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformations.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformations.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_context_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./color.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fractional_shift.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fractional_shift.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_completer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_property_mapper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_view.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/hhm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/hhm_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./null_data.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./null_data.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./polar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./polar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_helper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./line_average.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_average.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./observable.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./observable.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/pssm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pssm_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_tokenizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_tokenizer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./paste_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./paste_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./rscrosscorr.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./rscrosscorr.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_syntax_highlighter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./peak.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./peak.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/load.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/load.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./handle_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./phase.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./phase.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/save.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/save.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node.hh [ 1%] Built target ost_img_alg_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./ics_editor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./ics_editor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./physical_units.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./physical_units.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./binary_data_sink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_sink.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite2_op.cc.o -MF CMakeFiles/ost_geom.dir/composite2_op.cc.o.d -o CMakeFiles/ost_geom.dir/composite2_op.cc.o -c /build/openstructure-2.3.1/modules/geom/src/composite2_op.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./not_connected_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./not_connected_error.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./pixel_sampling.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./pixel_sampling.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_manager.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./point_list.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_text_document_layout.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./property_id.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./property_id.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./binary_data_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_source.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./point.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/shell_history.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./polygon_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./polygon_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/state_machine.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_error.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./container_serialization.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./container_serialization.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./progress.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./progress.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./swap_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./swap_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_state.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_prim.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./size.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./size.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_utils.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_utils.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/transition.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./symmetry_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./spherical_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./spherical_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_exception.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_exception.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_test_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.cc /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./util.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_prop.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./convert.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./convert.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glwin_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glwin_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/button_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_view.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./converting_streams.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./converting_streams.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./input.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./input.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./value_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./value_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/drop_box.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./formatted_line.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./formatted_line.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./sec_structure.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./sec_structure.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./prim_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./prim_list.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./vecmat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./vecmat.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./chemdict_parser.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_info_convert.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_info_convert.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./spatial_organizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_manager.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/star_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./star_parser.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./selection.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./selection.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/bottom_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/bottom_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_reader.hh [ 1%] Built target ost_img_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./surface.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/button_box.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_box.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_builder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_builder.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_info.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./texture.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./texture.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite3_op.cc.o -MF CMakeFiles/ost_geom.dir/composite3_op.cc.o.d -o CMakeFiles/ost_geom.dir/composite3_op.cc.o -c /build/openstructure-2.3.1/modules/geom/src/composite3_op.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/event_button.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/event_button.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./builder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./builder.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/io_profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_profile.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_widget_container.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_widget_container.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/dcd_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./dcd_io.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar_widget_holder.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_prop.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_crd_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/side_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/side_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./torsion_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./torsion_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene_observer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pqr_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/splitter_panel_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/splitter_panel_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transfer_connectivity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./transfer_connectivity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_include.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_include.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mae_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/tabbed_panel_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_view_wrapper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_view_wrapper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glext_include.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glext_include.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/context_menu.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_mode.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_mode.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_type_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/current_selection_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./material.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./material.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/custom_part_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./xcs_editor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./xcs_editor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pdb_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bounding_box.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bounding_box.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_writer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./transform.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_sdf_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_part_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./primitives.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./primitives.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_reader.hh [ 1%] Built target ost_mol_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/gfx_scene_node.hh In file included from /build/openstructure-2.3.1/modules/geom/src/composite2.hh:27, from /build/openstructure-2.3.1/modules/geom/src/composite2.cc:23: /build/openstructure-2.3.1/modules/geom/src/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/geom/src/def.hh:26, from /build/openstructure-2.3.1/modules/geom/src/composite2.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/modules/geom/src/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_writer.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/quat.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/quat.cc.o -MF CMakeFiles/ost_geom.dir/quat.cc.o.d -o CMakeFiles/ost_geom.dir/quat.cc.o -c /build/openstructure-2.3.1/modules/geom/src/quat.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/label_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/label_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/save_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./save_entity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/root_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/load_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_entity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_mode_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gost_exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_modes_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/load_surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_surface.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_msms_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_str.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_str.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_slab.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_slab.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/message_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_widget.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/omf.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./omf.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_box_widget.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh [ 1%] Built target ost_gfx_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/log_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/log_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o -MF CMakeFiles/ost_geom.dir/transform.cc.o.d -o CMakeFiles/ost_geom.dir/transform.cc.o -c /build/openstructure-2.3.1/modules/geom/src/transform.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/argand.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/argand.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pir_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./promod_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./profile_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/hhm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/draw_overlay.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/pssm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/clustal_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./clustal_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/drawing_functions.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/load.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/fft_panel.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/save.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./save.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/info_panel.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/load_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_map.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/img2qt.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_df3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_df3_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/mask_overlay.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/image_format.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./image_format.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/null_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/null_overlay.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dx_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_spi_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_spi_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_situs_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_situs_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_mrc_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_mrc_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dat_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_gui.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_gui.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_ipl_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_ipl_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_observer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_jpk_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_jpk_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_nanoscope_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dm3_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_tiff_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/tiff_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./tiff_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/viewer_normalizer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/jpk_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./jpk_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_browser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_browser.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_type_dialog.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_type_dialog.hh [ 1%] Built target ost_io_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_viewer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_viewer.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -MF CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o.d -o CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -c /build/openstructure-2.3.1/modules/geom/src/aligned_cuboid.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gl_canvas.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_canvas.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gl_win.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_win.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./scene_menu.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_menu.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gosty_app.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gosty_app.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./admin.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./admin.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main_area.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_area.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./perspective.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./perspective.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./scene_selection.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_selection.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main_window.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_window.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./thin_splitter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./thin_splitter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_geom_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_geom_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_pool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_pool.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_registry.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_registry.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_state_saver.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_state_saver.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_loader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_loader.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 1%] Built target ost_gui_headers [ 2%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o -MF CMakeFiles/ost_geom.dir/point_cloud.cc.o.d -o CMakeFiles/ost_geom.dir/point_cloud.cc.o -c /build/openstructure-2.3.1/modules/geom/src/point_cloud.cc In file included from /build/openstructure-2.3.1/modules/geom/src/composite2.hh:27, from /build/openstructure-2.3.1/modules/geom/src/composite2_op.hh:24, from /build/openstructure-2.3.1/modules/geom/src/composite2_op.cc:24: /build/openstructure-2.3.1/modules/geom/src/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/geom/src/composite2_op.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/modules/geom/src/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 2%] Linking CXX shared library ../../../stage/lib/libost_geom.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_geom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_geom.so.2.3 -o ../../../stage/lib/libost_geom.so.2.3.1 CMakeFiles/ost_geom.dir/mat2.cc.o CMakeFiles/ost_geom.dir/mat3.cc.o CMakeFiles/ost_geom.dir/mat4.cc.o CMakeFiles/ost_geom.dir/vec3.cc.o CMakeFiles/ost_geom.dir/vecmat2_op.cc.o CMakeFiles/ost_geom.dir/vecmat3_op.cc.o CMakeFiles/ost_geom.dir/vecmat4_op.cc.o CMakeFiles/ost_geom.dir/composite2.cc.o CMakeFiles/ost_geom.dir/composite3.cc.o CMakeFiles/ost_geom.dir/composite2_op.cc.o CMakeFiles/ost_geom.dir/composite3_op.cc.o CMakeFiles/ost_geom.dir/quat.cc.o CMakeFiles/ost_geom.dir/transform.cc.o CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o CMakeFiles/ost_geom.dir/point_cloud.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_geom.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3 ../../../stage/lib/libost_geom.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 2%] Built target ost_geom make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/ost_base.dir/DependInfo.cmake --color= make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod/CMakeFiles/_ost_geom.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/generic_property.cc.o [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/generic_property.cc.o -MF CMakeFiles/ost_base.dir/generic_property.cc.o.d -o CMakeFiles/ost_base.dir/generic_property.cc.o -c /build/openstructure-2.3.1/modules/base/src/generic_property.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec2.cc.o [ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log_sink.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/log.cc.o -MF CMakeFiles/ost_base.dir/log.cc.o.d -o CMakeFiles/ost_base.dir/log.cc.o -c /build/openstructure-2.3.1/modules/base/src/log.cc [ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/profile.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec2.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec2.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_vec2.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/log_sink.cc.o -MF CMakeFiles/ost_base.dir/log_sink.cc.o.d -o CMakeFiles/ost_base.dir/log_sink.cc.o -c /build/openstructure-2.3.1/modules/base/src/log_sink.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec3.cc.o [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o [ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/units.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat2_op.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/profile.cc.o -MF CMakeFiles/ost_base.dir/profile.cc.o.d -o CMakeFiles/ost_base.dir/profile.cc.o -c /build/openstructure-2.3.1/modules/base/src/profile.cc [ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/string_ref.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec3.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec3.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_vec3.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/units.cc.o -MF CMakeFiles/ost_base.dir/units.cc.o.d -o CMakeFiles/ost_base.dir/units.cc.o -c /build/openstructure-2.3.1/modules/base/src/units.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec4.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat3_op.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/string_ref.cc.o -MF CMakeFiles/ost_base.dir/string_ref.cc.o.d -o CMakeFiles/ost_base.dir/string_ref.cc.o -c /build/openstructure-2.3.1/modules/base/src/string_ref.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec4.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec4.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec4.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_vec4.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat4_op.cc [ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/message.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/message.cc.o -MF CMakeFiles/ost_base.dir/message.cc.o.d -o CMakeFiles/ost_base.dir/message.cc.o -c /build/openstructure-2.3.1/modules/base/src/message.cc [ 5%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/platform.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/platform.cc.o -MF CMakeFiles/ost_base.dir/platform.cc.o.d -o CMakeFiles/ost_base.dir/platform.cc.o -c /build/openstructure-2.3.1/modules/base/src/platform.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/wrap_geom.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/wrap_geom.cc.o -MF CMakeFiles/_ost_geom.dir/wrap_geom.cc.o.d -o CMakeFiles/_ost_geom.dir/wrap_geom.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/wrap_geom.cc [ 5%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o -MF CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o.d -o CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o -c /build/openstructure-2.3.1/modules/base/src/test_utils/compare_files.cc [ 5%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -MF CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o.d -o CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -c /build/openstructure-2.3.1/modules/base/src/boost_filesystem_helper.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat2.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat2.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat2.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_mat2.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat3.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat3.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat3.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_mat3.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat4.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat4.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat4.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat4.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_mat4.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite2.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_composite2.cc [ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite3.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_composite3.cc [ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_composite2_op.cc [ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_composite3_op.cc [ 6%] Linking CXX shared library ../../../stage/lib/libost_base.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_base.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_base.so.2.3 -o ../../../stage/lib/libost_base.so.2.3.1 CMakeFiles/ost_base.dir/generic_property.cc.o CMakeFiles/ost_base.dir/log.cc.o CMakeFiles/ost_base.dir/log_sink.cc.o CMakeFiles/ost_base.dir/profile.cc.o CMakeFiles/ost_base.dir/units.cc.o CMakeFiles/ost_base.dir/string_ref.cc.o CMakeFiles/ost_base.dir/platform.cc.o CMakeFiles/ost_base.dir/message.cc.o CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_base.so.2.3 ../../../stage/lib/libost_base.so In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/wrap_geom.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 6%] Built target ost_base make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src/CMakeFiles/ost_info.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_impl.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_impl.cc.o -MF CMakeFiles/ost_info.dir/info_impl.cc.o.d -o CMakeFiles/ost_info.dir/info_impl.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_impl.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat4_op.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/wrap_geom.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/export_vec3.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat4_op.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat3_op.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/export_vec2.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat2_op.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_vec3.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/export_vec4.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat3_op.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat2_op.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_vec2.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_vec4.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/export_mat2.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/export_mat3.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o -MF CMakeFiles/_ost_geom.dir/export_quat.cc.o.d -o CMakeFiles/_ost_geom.dir/export_quat.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_quat.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/info/src/info_impl.hh:41, from /build/openstructure-2.3.1/modules/info/src/info_impl.cc:37: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/info/src/info_impl.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/export_composite2.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_mat3.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_mat2.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/export_composite3.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o -MF CMakeFiles/_ost_geom.dir/export_transform.cc.o.d -o CMakeFiles/_ost_geom.dir/export_transform.cc.o -c /build/openstructure-2.3.1/modules/geom/pymod/export_transform.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/export_mat4.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_composite2.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/export_composite2_op.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/export_composite3_op.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_composite3.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_handle.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_handle.cc.o -MF CMakeFiles/ost_info.dir/info_handle.cc.o.d -o CMakeFiles/ost_info.dir/info_handle.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_handle.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_mat4.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_composite2_op.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_composite3_op.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_group.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_group.cc.o -MF CMakeFiles/ost_info.dir/info_group.cc.o.d -o CMakeFiles/ost_info.dir/info_group.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_group.cc [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_item.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_item.cc.o -MF CMakeFiles/ost_info.dir/info_item.cc.o.d -o CMakeFiles/ost_info.dir/info_item.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_item.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/info/src/info_group.hh:33, from /build/openstructure-2.3.1/modules/info/src/info.hh:32, from /build/openstructure-2.3.1/modules/info/src/info_handle.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/info/src/info_handle.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/export_quat.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_path.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_path.cc.o -MF CMakeFiles/ost_info.dir/info_path.cc.o.d -o CMakeFiles/ost_info.dir/info_path.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_path.cc [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_set.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_set.cc.o -MF CMakeFiles/ost_info.dir/info_set.cc.o.d -o CMakeFiles/ost_info.dir/info_set.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_set.cc [ 7%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_visitor.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_visitor.cc.o -MF CMakeFiles/ost_info.dir/info_visitor.cc.o.d -o CMakeFiles/ost_info.dir/info_visitor.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_visitor.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_quat.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 7%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -MF CMakeFiles/ost_info.dir/geom_info_conversion.cc.o.d -o CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -c /build/openstructure-2.3.1/modules/info/src/geom_info_conversion.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/geom/pymod/export_transform.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 7%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -MF CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o.d -o CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -c /build/openstructure-2.3.1/modules/info/src/info_verbose_visitor.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/info/src/info_group.hh:33, from /build/openstructure-2.3.1/modules/info/src/info.hh:32, from /build/openstructure-2.3.1/modules/info/src/info_group.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/modules/info/src/info_handle.hh:31, from /build/openstructure-2.3.1/modules/info/src/info.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/info/src/info_group.hh:33, from /build/openstructure-2.3.1/modules/info/src/info.hh:32, from /build/openstructure-2.3.1/modules/info/src/info_item.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/info/src/info_item.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/info/src/info_group.hh:33, from /build/openstructure-2.3.1/modules/info/src/info_set.hh:29, from /build/openstructure-2.3.1/modules/info/src/info_set.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/info/src/info_set.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/info/src/geom_info_conversion.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_handle.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/info/src/info_group.hh:33, from /build/openstructure-2.3.1/modules/info/src/info_verbose_visitor.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/info/src/info_verbose_visitor.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 7%] Linking CXX shared library ../../../stage/lib/libost_info.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_info.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_info.so.2.3 -o ../../../stage/lib/libost_info.so.2.3.1 CMakeFiles/ost_info.dir/info_impl.cc.o CMakeFiles/ost_info.dir/info_handle.cc.o CMakeFiles/ost_info.dir/info_group.cc.o CMakeFiles/ost_info.dir/info_item.cc.o CMakeFiles/ost_info.dir/info_path.cc.o CMakeFiles/ost_info.dir/info_set.cc.o CMakeFiles/ost_info.dir/info_visitor.cc.o CMakeFiles/ost_info.dir/geom_info_conversion.cc.o CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_info.so.2.3 ../../../stage/lib/libost_info.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 7%] Built target ost_info make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/depend make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/circle_mask.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o -MF CMakeFiles/ost_mol.dir/atom_base.cc.o.d -o CMakeFiles/ost_mol.dir/atom_base.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/atom_base.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/composite_mask.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/circle_mask.cc.o -MF CMakeFiles/ost_img.dir/circle_mask.cc.o.d -o CMakeFiles/ost_img.dir/circle_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/circle_mask.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o -MF CMakeFiles/ost_mol.dir/atom_handle.cc.o.d -o CMakeFiles/ost_mol.dir/atom_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/atom_handle.cc [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_algorithm.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/composite_mask.cc.o -MF CMakeFiles/ost_img.dir/composite_mask.cc.o.d -o CMakeFiles/ost_img.dir/composite_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/composite_mask.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o -MF CMakeFiles/ost_mol.dir/atom_view.cc.o.d -o CMakeFiles/ost_mol.dir/atom_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/atom_view.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data_algorithm.cc.o -MF CMakeFiles/ost_img.dir/data_algorithm.cc.o.d -o CMakeFiles/ost_img.dir/data_algorithm.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/data_algorithm.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o -MF CMakeFiles/ost_img.dir/data_observer.cc.o.d -o CMakeFiles/ost_img.dir/data_observer.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/data_observer.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o -MF CMakeFiles/ost_img.dir/data.cc.o.d -o CMakeFiles/ost_img.dir/data.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/data.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o -MF CMakeFiles/ost_mol.dir/bond_handle.cc.o.d -o CMakeFiles/ost_mol.dir/bond_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/bond_handle.cc [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_iterator.cc.o [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o -MF CMakeFiles/ost_mol.dir/chain_base.cc.o.d -o CMakeFiles/ost_mol.dir/chain_base.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/chain_base.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent_iterator.cc.o -MF CMakeFiles/ost_img.dir/extent_iterator.cc.o.d -o CMakeFiles/ost_img.dir/extent_iterator.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/extent_iterator.cc [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o -MF CMakeFiles/ost_img.dir/extent_mask.cc.o.d -o CMakeFiles/ost_img.dir/extent_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/extent_mask.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o -MF CMakeFiles/ost_mol.dir/chain_handle.cc.o.d -o CMakeFiles/ost_mol.dir/chain_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.cc [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o -MF CMakeFiles/ost_mol.dir/chain_view.cc.o.d -o CMakeFiles/ost_mol.dir/chain_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/chain_view.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent.cc.o -MF CMakeFiles/ost_img.dir/extent.cc.o.d -o CMakeFiles/ost_img.dir/extent.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/extent.cc In file included from /usr/include/boost/bind.hpp:30, from /build/openstructure-2.3.1/modules/mol/base/src/chain_view.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/extent_mask.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/extent_mask.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/img/base/src/extent.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/extent_iterator.hh:30, from /build/openstructure-2.3.1/modules/img/base/src/extent_iterator.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/data.hh:36, from /build/openstructure-2.3.1/modules/img/base/src/image_handle.hh:38, from /build/openstructure-2.3.1/modules/img/base/src/data_observer.hh:31, from /build/openstructure-2.3.1/modules/img/base/src/data_observer.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/base/src/data_observer.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, from /build/openstructure-2.3.1/modules/img/base/src/composite_mask.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/composite_mask.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/atom_handle.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/atom_handle.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/atom_handle.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/data.hh:36, from /build/openstructure-2.3.1/modules/img/base/src/data.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/img/base/src/data.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/circle_mask.hh:25, from /build/openstructure-2.3.1/modules/img/base/src/circle_mask.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/atom_base.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/atom_base.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/atom_base.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/chain_base.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/chain_base.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/chain_base.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 10%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/geom/_ost_geom.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_geom.dir/link.txt --verbose=1 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/modules/mol/base/src/residue_view.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/atom_view.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/atom_view.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/atom_view.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/geom/_ost_geom.so CMakeFiles/_ost_geom.dir/export_vec2.cc.o CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o CMakeFiles/_ost_geom.dir/export_vec3.cc.o CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o CMakeFiles/_ost_geom.dir/export_vec4.cc.o CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o CMakeFiles/_ost_geom.dir/wrap_geom.cc.o CMakeFiles/_ost_geom.dir/export_mat2.cc.o CMakeFiles/_ost_geom.dir/export_mat3.cc.o CMakeFiles/_ost_geom.dir/export_mat4.cc.o CMakeFiles/_ost_geom.dir/export_composite2.cc.o CMakeFiles/_ost_geom.dir/export_composite3.cc.o CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o CMakeFiles/_ost_geom.dir/export_quat.cc.o CMakeFiles/_ost_geom.dir/export_transform.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/bond_handle.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/list:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/bond_handle.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/bond_handle.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/chain_view.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /build/openstructure-2.3.1/modules/mol/base/src/chain_view.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/extent.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/base/src/extent.cc:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o -MF CMakeFiles/ost_img.dir/image_factory.cc.o.d -o CMakeFiles/ost_img.dir/image_factory.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_factory.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o -MF CMakeFiles/ost_img.dir/image_handle.cc.o.d -o CMakeFiles/ost_img.dir/image_handle.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_handle.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o -MF CMakeFiles/ost_img.dir/image_impl.cc.o.d -o CMakeFiles/ost_img.dir/image_impl.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_impl.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o -MF CMakeFiles/ost_img.dir/image_list.cc.o.d -o CMakeFiles/ost_img.dir/image_list.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_list.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o -MF CMakeFiles/ost_img.dir/inverted_mask.cc.o.d -o CMakeFiles/ost_img.dir/inverted_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/inverted_mask.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/geom/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/geom/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 10%] Built target _ost_geom make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/_ost_base.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 10%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o -MF CMakeFiles/_ost_base.dir/wrap_base.cc.o.d -o CMakeFiles/_ost_base.dir/wrap_base.cc.o -c /build/openstructure-2.3.1/modules/base/pymod/wrap_base.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o -MF CMakeFiles/ost_img.dir/map.cc.o.d -o CMakeFiles/ost_img.dir/map.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/map.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o -MF CMakeFiles/ost_mol.dir/chain_type.cc.o.d -o CMakeFiles/ost_mol.dir/chain_type.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/chain_type.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o -MF CMakeFiles/ost_mol.dir/coord_frame.cc.o.d -o CMakeFiles/ost_mol.dir/coord_frame.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/coord_frame.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o -MF CMakeFiles/ost_mol.dir/coord_group.cc.o.d -o CMakeFiles/ost_mol.dir/coord_group.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/coord_group.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o -MF CMakeFiles/ost_mol.dir/editor_base.cc.o.d -o CMakeFiles/ost_mol.dir/editor_base.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/editor_base.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o -MF CMakeFiles/ost_img.dir/mask_base.cc.o.d -o CMakeFiles/ost_img.dir/mask_base.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/mask_base.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, from /build/openstructure-2.3.1/modules/img/base/src/inverted_mask.hh:23, from /build/openstructure-2.3.1/modules/img/base/src/inverted_mask.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o -MF CMakeFiles/ost_mol.dir/entity_base.cc.o.d -o CMakeFiles/ost_mol.dir/entity_base.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_base.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o -MF CMakeFiles/ost_mol.dir/entity_handle.cc.o.d -o CMakeFiles/ost_mol.dir/entity_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_handle.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/image_list.hh:29, from /build/openstructure-2.3.1/modules/img/base/src/image_list.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/openstructure-2.3.1/modules/img/base/src/image_list.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh:31, from /build/openstructure-2.3.1/modules/img/base/src/image_state_fw.hh:30, from /build/openstructure-2.3.1/modules/img/base/src/image_impl.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/image_impl.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/modules/img/base/src/image_impl.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/map.hh:22, from /build/openstructure-2.3.1/modules/img/base/src/map.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:32: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/image_factory.hh:32, from /build/openstructure-2.3.1/modules/img/base/src/image_factory.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/img/base/src/image_factory.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/data.hh:36, from /build/openstructure-2.3.1/modules/img/base/src/image_handle.hh:38, from /build/openstructure-2.3.1/modules/img/base/src/image_handle.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/img/base/src/image_handle.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/in_mem_coord_source.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/coord_frame.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/coord_frame.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, from /build/openstructure-2.3.1/modules/img/base/src/mask_base.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/coord_group.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/coord_group.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/editor_base.hh:27, from /build/openstructure-2.3.1/modules/mol/base/src/editor_base.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/editor_base.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o -MF CMakeFiles/ost_img.dir/mask_op.cc.o.d -o CMakeFiles/ost_img.dir/mask_op.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/mask_op.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask.cc.o -MF CMakeFiles/ost_img.dir/mask.cc.o.d -o CMakeFiles/ost_img.dir/mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/mask.cc [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o -MF CMakeFiles/ost_img.dir/observable.cc.o.d -o CMakeFiles/ost_img.dir/observable.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/observable.cc In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/editor_base.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o -MF CMakeFiles/ost_img.dir/paste_impl.cc.o.d -o CMakeFiles/ost_img.dir/paste_impl.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/paste_impl.cc [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o -MF CMakeFiles/ost_img.dir/peak.cc.o.d -o CMakeFiles/ost_img.dir/peak.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/peak.cc [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o -MF CMakeFiles/ost_img.dir/phase.cc.o.d -o CMakeFiles/ost_img.dir/phase.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/phase.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/entity_handle.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/entity_handle.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o -MF CMakeFiles/ost_mol.dir/entity_observer.cc.o.d -o CMakeFiles/ost_mol.dir/entity_observer.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_observer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/entity_base.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/entity_base.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/entity_base.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o -MF CMakeFiles/ost_img.dir/physical_units.cc.o.d -o CMakeFiles/ost_img.dir/physical_units.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/physical_units.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/base/pymod/wrap_base.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/mask.hh:29, from /build/openstructure-2.3.1/modules/img/base/src/mask.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/img/base/src/mask.hh:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, from /build/openstructure-2.3.1/modules/img/base/src/composite_mask.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/mask_op.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/scoped_ptr.hpp:22, from /usr/include/boost/scoped_ptr.hpp:13, from /usr/include/boost/smart_ptr.hpp:17, from /build/openstructure-2.3.1/modules/img/base/src/mask_base_fw.hh:23, from /build/openstructure-2.3.1/modules/img/base/src/mask_op.hh:24, from /build/openstructure-2.3.1/modules/img/base/src/mask_op.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/observable.hh:31, from /build/openstructure-2.3.1/modules/img/base/src/observable.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/list:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/observable.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_algorithm.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/paste_impl.hh:24, from /build/openstructure-2.3.1/modules/img/base/src/paste_impl.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:32: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -MF CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o.d -o CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.cc [ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o -MF CMakeFiles/ost_mol.dir/entity_view.cc.o.d -o CMakeFiles/ost_mol.dir/entity_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc [ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o -MF CMakeFiles/ost_mol.dir/entity_visitor.cc.o.d -o CMakeFiles/ost_mol.dir/entity_visitor.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/entity_visitor.cc [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/pixel_sampling.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/pixel_sampling.cc.o -MF CMakeFiles/ost_img.dir/pixel_sampling.cc.o.d -o CMakeFiles/ost_img.dir/pixel_sampling.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/pixel_sampling.cc [ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o -MF CMakeFiles/ost_mol.dir/ics_editor.cc.o.d -o CMakeFiles/ost_mol.dir/ics_editor.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/peak.hh:31, from /build/openstructure-2.3.1/modules/img/base/src/peak.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/openstructure-2.3.1/modules/img/base/src/peak.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o -MF CMakeFiles/ost_mol.dir/not_connected_error.cc.o.d -o CMakeFiles/ost_mol.dir/not_connected_error.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/not_connected_error.cc [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o -MF CMakeFiles/ost_img.dir/point_list.cc.o.d -o CMakeFiles/ost_img.dir/point_list.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/point_list.cc [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o -MF CMakeFiles/ost_img.dir/point.cc.o.d -o CMakeFiles/ost_img.dir/point.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/point.cc [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o -MF CMakeFiles/ost_img.dir/polygon_mask.cc.o.d -o CMakeFiles/ost_img.dir/polygon_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.cc [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o -MF CMakeFiles/ost_img.dir/progress.cc.o.d -o CMakeFiles/ost_img.dir/progress.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/progress.cc [ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o -MF CMakeFiles/ost_mol.dir/property_id.cc.o.d -o CMakeFiles/ost_mol.dir/property_id.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/property_id.cc In file included from /usr/include/boost/bind.hpp:30, from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o -MF CMakeFiles/ost_mol.dir/query.cc.o.d -o CMakeFiles/ost_mol.dir/query.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/query.cc [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o -MF CMakeFiles/ost_img.dir/size.cc.o.d -o CMakeFiles/ost_img.dir/size.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/size.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/pixel_sampling.hh:32, from /build/openstructure-2.3.1/modules/img/base/src/pixel_sampling.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/openstructure-2.3.1/modules/img/base/src/pixel_sampling.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o -MF CMakeFiles/ost_img.dir/spherical_mask.cc.o.d -o CMakeFiles/ost_img.dir/spherical_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/spherical_mask.cc [ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o -MF CMakeFiles/ost_img.dir/mask_info_convert.cc.o.d -o CMakeFiles/ost_img.dir/mask_info_convert.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/mask_info_convert.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.hh:29, from /build/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.hh:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/point_list.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/point_list.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o -MF CMakeFiles/ost_mol.dir/query_error.cc.o.d -o CMakeFiles/ost_mol.dir/query_error.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/query_error.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/point.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/img/base/src/point.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:40: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o -MF CMakeFiles/ost_mol.dir/query_state.cc.o.d -o CMakeFiles/ost_mol.dir/query_state.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/query_state.cc [ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -MF CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o.d -o CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.cc [ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o -MF CMakeFiles/ost_mol.dir/residue_base.cc.o.d -o CMakeFiles/ost_mol.dir/residue_base.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/residue_base.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/size.cc:32: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/img/base/src/size.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o -MF CMakeFiles/ost_mol.dir/residue_handle.cc.o.d -o CMakeFiles/ost_mol.dir/residue_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/residue_handle.cc [ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o -MF CMakeFiles/ost_img.dir/image_state/index.cc.o.d -o CMakeFiles/ost_img.dir/image_state/index.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_state/index.cc [ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -MF CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o.d -o CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.cc [ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_view.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_view.cc.o -MF CMakeFiles/ost_mol.dir/residue_view.cc.o.d -o CMakeFiles/ost_mol.dir/residue_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/residue_view.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/spherical_mask.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/spherical_mask.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/query.hh:39, from /build/openstructure-2.3.1/modules/mol/base/src/query.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/modules/mol/base/src/query.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -MF CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o.d -o CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -c /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.cc [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_builder.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_builder.cc.o -MF CMakeFiles/ost_mol.dir/surface_builder.cc.o.d -o CMakeFiles/ost_mol.dir/surface_builder.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/surface_builder.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/img/base/src/mask_info_convert.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/deque:60, from /usr/include/c++/12/stack:60, from /build/openstructure-2.3.1/modules/img/base/src/mask_info_convert.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_handle.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_handle.cc.o -MF CMakeFiles/ost_mol.dir/surface_handle.cc.o.d -o CMakeFiles/ost_mol.dir/surface_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/surface_handle.cc In file included from /usr/include/boost/bind.hpp:30, from /build/openstructure-2.3.1/modules/mol/base/src/residue_view.cc:22: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/query_state.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/residue_base.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/residue_base.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -MF CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o.d -o CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh:31, from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data_types.hh:30, from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/query_state.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o -MF CMakeFiles/ost_mol.dir/torsion_handle.cc.o.d -o CMakeFiles/ost_mol.dir/torsion_handle.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/torsion_handle.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/residue_handle.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base_fw.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/residue_handle.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/modules/mol/base/src/residue_view.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /build/openstructure-2.3.1/modules/mol/base/src/residue_view.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.hh:31, from /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.cc:38: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.cc:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/surface_handle.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/surface_builder.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/surface_builder.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/surface_builder.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -MF CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o.d -o CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/query_view_wrapper.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/surface_handle.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/query.hh:39, from /build/openstructure-2.3.1/modules/mol/base/src/entity_handle.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/module_config.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/view_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/view_op.cc.o -MF CMakeFiles/ost_mol.dir/view_op.cc.o.d -o CMakeFiles/ost_mol.dir/view_op.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/view_op.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/torsion_handle.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/torsion_handle.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/torsion_handle.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o -MF CMakeFiles/ost_mol.dir/coord_source.cc.o.d -o CMakeFiles/ost_mol.dir/coord_source.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/coord_source.cc [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -MF CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o.d -o CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.cc [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o -MF CMakeFiles/ost_mol.dir/bounding_box.cc.o.d -o CMakeFiles/ost_mol.dir/bounding_box.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/bounding_box.cc [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o -MF CMakeFiles/ost_mol.dir/xcs_editor.cc.o.d -o CMakeFiles/ost_mol.dir/xcs_editor.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.cc [ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/base/src/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/query_view_wrapper.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/query_view_wrapper.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/view_op.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/mol/base/src/view_op.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/view_op.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -MF CMakeFiles/ost_mol.dir/impl/dihedral.cc.o.d -o CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/coord_source.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/coord_source.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o -MF CMakeFiles/ost_mol.dir/impl/query_ast.cc.o.d -o CMakeFiles/ost_mol.dir/impl/query_ast.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log_sink.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/weak_ptr.hpp:16, from /usr/include/boost/smart_ptr/enable_shared_from_this.hpp:16, from /usr/include/boost/enable_shared_from_this.hpp:16, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/query_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log_sink.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/bounding_box.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/eigen3/Eigen/src/Core/util/Macros.h:679, from /usr/include/eigen3/Eigen/Core:19, from /usr/include/eigen3/Eigen/Eigenvalues:11, from /build/openstructure-2.3.1/modules/mol/base/src/bounding_box.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc:35: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 16%] Linking CXX shared library ../../../../stage/lib/libost_img.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_img.so.2.3 -o ../../../../stage/lib/libost_img.so.2.3.1 CMakeFiles/ost_img.dir/circle_mask.cc.o CMakeFiles/ost_img.dir/composite_mask.cc.o CMakeFiles/ost_img.dir/data_algorithm.cc.o CMakeFiles/ost_img.dir/data_observer.cc.o CMakeFiles/ost_img.dir/data.cc.o CMakeFiles/ost_img.dir/extent_iterator.cc.o CMakeFiles/ost_img.dir/extent_mask.cc.o CMakeFiles/ost_img.dir/extent.cc.o CMakeFiles/ost_img.dir/image_factory.cc.o CMakeFiles/ost_img.dir/image_handle.cc.o CMakeFiles/ost_img.dir/image_impl.cc.o CMakeFiles/ost_img.dir/image_list.cc.o CMakeFiles/ost_img.dir/inverted_mask.cc.o CMakeFiles/ost_img.dir/map.cc.o CMakeFiles/ost_img.dir/mask_base.cc.o CMakeFiles/ost_img.dir/mask_op.cc.o CMakeFiles/ost_img.dir/mask.cc.o CMakeFiles/ost_img.dir/observable.cc.o CMakeFiles/ost_img.dir/paste_impl.cc.o CMakeFiles/ost_img.dir/peak.cc.o CMakeFiles/ost_img.dir/phase.cc.o CMakeFiles/ost_img.dir/physical_units.cc.o CMakeFiles/ost_img.dir/pixel_sampling.cc.o CMakeFiles/ost_img.dir/point_list.cc.o CMakeFiles/ost_img.dir/point.cc.o CMakeFiles/ost_img.dir/polygon_mask.cc.o CMakeFiles/ost_img.dir/progress.cc.o CMakeFiles/ost_img.dir/size.cc.o CMakeFiles/ost_img.dir/spherical_mask.cc.o CMakeFiles/ost_img.dir/mask_info_convert.cc.o CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o CMakeFiles/ost_img.dir/image_state/index.cc.o CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 [ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.cc [ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc:40: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3 ../../../../stage/lib/libost_img.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 16%] Built target ost_img make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -MF CMakeFiles/ost_img_alg.dir/anisotropic.cc.o.d -o CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/anisotropic.cc [ 17%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -MF CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o.d -o CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -c /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_prop.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/auto_correlate.cc [ 17%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o -MF CMakeFiles/_ost_base.dir/export_logger.cc.o.d -o CMakeFiles/_ost_base.dir/export_logger.cc.o -c /build/openstructure-2.3.1/modules/base/pymod/export_logger.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log_sink.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 17%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o -MF CMakeFiles/_ost_base.dir/export_range.cc.o.d -o CMakeFiles/_ost_base.dir/export_range.cc.o -c /build/openstructure-2.3.1/modules/base/pymod/export_range.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian.hh:36, from /build/openstructure-2.3.1/modules/img/alg/src/anisotropic.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/anisotropic.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/img/alg/src/anisotropic.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh:36, from /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o -MF CMakeFiles/ost_img_alg.dir/convolute.cc.o.d -o CMakeFiles/ost_img_alg.dir/convolute.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/convolute.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/correlate.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/correlate.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/correlate.cc [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/cross_correlate.cc [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/density_slice.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/density_slice.cc.o -MF CMakeFiles/ost_img_alg.dir/density_slice.cc.o.d -o CMakeFiles/ost_img_alg.dir/density_slice.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/density_slice.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/fft.hh:27, from /build/openstructure-2.3.1/modules/img/alg/src/auto_correlate.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/img/alg/src/auto_correlate.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 19%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o -MF CMakeFiles/_ost_base.dir/export_units.cc.o.d -o CMakeFiles/_ost_base.dir/export_units.cc.o -c /build/openstructure-2.3.1/modules/base/pymod/export_units.cc [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o -MF CMakeFiles/ost_img_alg.dir/dft.cc.o.d -o CMakeFiles/ost_img_alg.dir/dft.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/dft.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/convolute.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/convolute.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/cross_correlate.hh:27, from /build/openstructure-2.3.1/modules/img/alg/src/cross_correlate.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o -MF CMakeFiles/ost_img_alg.dir/fft.cc.o.d -o CMakeFiles/ost_img_alg.dir/fft.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/fft.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/correlate.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/correlate.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/base/pymod/export_range.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/base/pymod/export_logger.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/density_slice.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/density_slice.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/dft.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/dft.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o -MF CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o.d -o CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/fourier_filters.cc [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/gaussian.cc [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/gaussian_gradient_magnitude.cc [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/fft.cc:36: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/openstructure-2.3.1/modules/img/alg/src/fft.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -MF CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o.d -o CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/highest_peak_search_3d.cc [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/histogram.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/histogram.cc.o -MF CMakeFiles/ost_img_alg.dir/histogram.cc.o.d -o CMakeFiles/ost_img_alg.dir/histogram.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/histogram.cc [ 19%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_iterator.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_iterator.cc.o -MF CMakeFiles/ost_img_alg.dir/line_iterator.cc.o.d -o CMakeFiles/ost_img_alg.dir/line_iterator.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/line_iterator.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/base/pymod/export_units.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -MF CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o.d -o CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/local_sigma_threshold.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, from /build/openstructure-2.3.1/modules/img/alg/src/fourier_filters.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/img/alg/src/fourier_filters.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Linking CXX shared library ../../../../stage/lib/libost_mol.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol.so.2.3 -o ../../../../stage/lib/libost_mol.so.2.3.1 CMakeFiles/ost_mol.dir/atom_base.cc.o CMakeFiles/ost_mol.dir/atom_handle.cc.o CMakeFiles/ost_mol.dir/atom_view.cc.o CMakeFiles/ost_mol.dir/bond_handle.cc.o CMakeFiles/ost_mol.dir/chain_base.cc.o CMakeFiles/ost_mol.dir/chain_handle.cc.o CMakeFiles/ost_mol.dir/chain_view.cc.o CMakeFiles/ost_mol.dir/chain_type.cc.o CMakeFiles/ost_mol.dir/coord_frame.cc.o CMakeFiles/ost_mol.dir/coord_group.cc.o CMakeFiles/ost_mol.dir/editor_base.cc.o CMakeFiles/ost_mol.dir/entity_base.cc.o CMakeFiles/ost_mol.dir/entity_handle.cc.o CMakeFiles/ost_mol.dir/entity_observer.cc.o CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o CMakeFiles/ost_mol.dir/entity_view.cc.o CMakeFiles/ost_mol.dir/entity_visitor.cc.o CMakeFiles/ost_mol.dir/ics_editor.cc.o CMakeFiles/ost_mol.dir/not_connected_error.cc.o CMakeFiles/ost_mol.dir/property_id.cc.o CMakeFiles/ost_mol.dir/query.cc.o CMakeFiles/ost_mol.dir/query_error.cc.o CMakeFiles/ost_mol.dir/query_state.cc.o CMakeFiles/ost_mol.dir/residue_base.cc.o CMakeFiles/ost_mol.dir/residue_handle.cc.o CMakeFiles/ost_mol.dir/residue_view.cc.o CMakeFiles/ost_mol.dir/surface_builder.cc.o CMakeFiles/ost_mol.dir/surface_handle.cc.o CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o CMakeFiles/ost_mol.dir/torsion_handle.cc.o CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o CMakeFiles/ost_mol.dir/view_op.cc.o CMakeFiles/ost_mol.dir/coord_source.cc.o CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o CMakeFiles/ost_mol.dir/bounding_box.cc.o CMakeFiles/ost_mol.dir/xcs_editor.cc.o CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o CMakeFiles/ost_mol.dir/impl/dihedral.cc.o CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o CMakeFiles/ost_mol.dir/impl/query_ast.cc.o CMakeFiles/ost_mol.dir/impl/query_impl.cc.o CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian.hh:36, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o -MF CMakeFiles/ost_img_alg.dir/mask_image.cc.o.d -o CMakeFiles/ost_img_alg.dir/mask_image.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/mask_image.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_gradient_magnitude.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_gradient_magnitude.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_gradient_magnitude.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3 ../../../../stage/lib/libost_mol.so In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/img/alg/src/line_iterator.hh:29, from /build/openstructure-2.3.1/modules/img/alg/src/line_iterator.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 20%] Built target ost_mol make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 20%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer.cc.o -MF CMakeFiles/ost_img_alg.dir/normalizer.cc.o.d -o CMakeFiles/ost_img_alg.dir/normalizer.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/normalizer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -MF CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o.d -o CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/normalizer_factory.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, from /build/openstructure-2.3.1/modules/img/alg/src/highest_peak_search_3d.cc:4: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/alg/src/highest_peak_search_3d.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/stat.hh:30, from /build/openstructure-2.3.1/modules/img/alg/src/histogram.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/img/alg/src/histogram.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_linear.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/norm_linear.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_log.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_log.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/norm_log.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/local_sigma_threshold.hh:23, from /build/openstructure-2.3.1/modules/img/alg/src/local_sigma_threshold.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/alg/src/local_sigma_threshold.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_od.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_od.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/norm_od.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -MF CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o.d -o CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/power_spectrum.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/mask_image.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o -MF CMakeFiles/ost_img_alg.dir/randomize.cc.o.d -o CMakeFiles/ost_img_alg.dir/randomize.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/randomize.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o -MF CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o.d -o CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/smooth_mask_image.cc [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat.cc.o -MF CMakeFiles/ost_img_alg.dir/stat.cc.o.d -o CMakeFiles/ost_img_alg.dir/stat.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/stat.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat_min_max.hh:30, from /build/openstructure-2.3.1/modules/img/alg/src/normalizer_factory.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/normalizer.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/normalizer.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o -MF CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o.d -o CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/stat_min_max.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /usr/include/boost/format.hpp:17, from /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_transform.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/alg_transform.cc [ 21%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/_ost_base.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_base.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/_ost_base.so CMakeFiles/_ost_base.dir/wrap_base.cc.o CMakeFiles/_ost_base.dir/export_logger.cc.o CMakeFiles/_ost_base.dir/export_range.cc.o CMakeFiles/_ost_base.dir/export_units.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_base.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/alg_mirror.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/norm_linear.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/norm_linear.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_shift.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_shift.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/alg_shift.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/settings.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.pyc\",\"settings.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/stutil.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.pyc\",\"stutil.py\",doraise=True)" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/norm_log.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/norm_log.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/table.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.pyc\",\"table.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/table_selector.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.pyc\",\"table_selector.py\",doraise=True)" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/norm_od.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/norm_od.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/xmlrunner.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.pyc\",\"xmlrunner.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/testutils.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.pyc\",\"testutils.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 21%] Built target _ost_base make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 21%] Building CXX object modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_info_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o -MF CMakeFiles/_ost_info.dir/wrap_info.cc.o.d -o CMakeFiles/_ost_info.dir/wrap_info.cc.o -c /build/openstructure-2.3.1/modules/info/pymod/wrap_info.cc [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o -MF CMakeFiles/ost_img_alg.dir/threshold.cc.o.d -o CMakeFiles/ost_img_alg.dir/threshold.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/threshold.cc [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -MF CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o.d -o CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/fft.hh:27, from /build/openstructure-2.3.1/modules/img/alg/src/power_spectrum.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/img/alg/src/power_spectrum.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/randomize.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/randomize.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/smooth_mask_image.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -MF CMakeFiles/ost_img_alg.dir/transformation_base.cc.o.d -o CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.cc [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o -MF CMakeFiles/ost_img_alg.dir/transformations.cc.o.d -o CMakeFiles/ost_img_alg.dir/transformations.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/transformations.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/stat_min_max.hh:30, from /build/openstructure-2.3.1/modules/img/alg/src/stat_min_max.cc:32: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/img/alg/src/stat_min_max.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/alg_mirror.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/alg_mirror.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -MF CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o.d -o CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/fractional_shift.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/stat.hh:30, from /build/openstructure-2.3.1/modules/img/alg/src/stat.cc:32: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/img/alg/src/stat.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/alg_transform.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/alg_transform.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o -MF CMakeFiles/ost_img_alg.dir/polar.cc.o.d -o CMakeFiles/ost_img_alg.dir/polar.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/polar.cc [ 23%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -MF CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o.d -o CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/rscrosscorr.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/alg_shift.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/alg_shift.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/threshold.hh:25, from /build/openstructure-2.3.1/modules/img/alg/src/threshold.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o -MF CMakeFiles/ost_img_alg.dir/line_average.cc.o.d -o CMakeFiles/ost_img_alg.dir/line_average.cc.o -c /build/openstructure-2.3.1/modules/img/alg/src/line_average.cc [ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/transformations.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/transformations.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/img/alg/src/transformations.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_handle.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_handle.cc.o -MF CMakeFiles/ost_seq.dir/sequence_handle.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_handle.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/sequence_handle.cc [ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o -MF CMakeFiles/ost_seq.dir/aligned_region.cc.o.d -o CMakeFiles/ost_seq.dir/aligned_region.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/aligned_region.cc [ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_column.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_column.cc.o -MF CMakeFiles/ost_seq.dir/aligned_column.cc.o.d -o CMakeFiles/ost_seq.dir/aligned_column.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/aligned_column.cc [ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o -MF CMakeFiles/ost_seq.dir/sequence_list.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_list.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc [ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o -MF CMakeFiles/ost_seq.dir/alignment_handle.cc.o.d -o CMakeFiles/ost_seq.dir/alignment_handle.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc [ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_op.cc.o -MF CMakeFiles/ost_seq.dir/sequence_op.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_op.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/sequence_op.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, from /build/openstructure-2.3.1/modules/img/alg/src/fractional_shift.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/img/alg/src/fractional_shift.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/polar.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/polar.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/modules/img/alg/src/polar.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/views_from_sequences.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/views_from_sequences.cc.o -MF CMakeFiles/ost_seq.dir/views_from_sequences.cc.o.d -o CMakeFiles/ost_seq.dir/views_from_sequences.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/views_from_sequences.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/rscrosscorr.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/info/pymod/wrap_info.cc:27: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_handle.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/img/alg/src/line_average.hh:23, from /build/openstructure-2.3.1/modules/img/alg/src/line_average.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o -MF CMakeFiles/ost_seq.dir/profile_handle.cc.o.d -o CMakeFiles/ost_seq.dir/profile_handle.cc.o -c /build/openstructure-2.3.1/modules/seq/base/src/profile_handle.cc In file included from /usr/include/boost/bind.hpp:30, from /build/openstructure-2.3.1/modules/seq/base/src/sequence_op.cc:22: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/openstructure-2.3.1/modules/seq/base/src/aligned_column.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:26, from /build/openstructure-2.3.1/modules/seq/base/src/aligned_region.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/integrity_error.hh:22, from /build/openstructure-2.3.1/modules/seq/base/src/aligned_region.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/modules/seq/base/src/sequence_handle.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/openstructure-2.3.1/modules/seq/base/src/sequence_handle.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc:32: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/seq/base/src/sequence_op.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/openstructure-2.3.1/modules/seq/base/src/sequence_op.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/views_from_sequences.hh:23, from /build/openstructure-2.3.1/modules/seq/base/src/views_from_sequences.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/integrity_error.hh:22, from /build/openstructure-2.3.1/modules/seq/base/src/views_from_sequences.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Linking CXX shared library ../../../../stage/lib/libost_img_alg.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_img_alg.so.2.3 -o ../../../../stage/lib/libost_img_alg.so.2.3.1 CMakeFiles/ost_img_alg.dir/anisotropic.cc.o CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o CMakeFiles/ost_img_alg.dir/convolute.cc.o CMakeFiles/ost_img_alg.dir/correlate.cc.o CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o CMakeFiles/ost_img_alg.dir/density_slice.cc.o CMakeFiles/ost_img_alg.dir/dft.cc.o CMakeFiles/ost_img_alg.dir/fft.cc.o CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o CMakeFiles/ost_img_alg.dir/gaussian.cc.o CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o CMakeFiles/ost_img_alg.dir/histogram.cc.o CMakeFiles/ost_img_alg.dir/line_iterator.cc.o CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o CMakeFiles/ost_img_alg.dir/mask_image.cc.o CMakeFiles/ost_img_alg.dir/normalizer.cc.o CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o CMakeFiles/ost_img_alg.dir/norm_linear.cc.o CMakeFiles/ost_img_alg.dir/norm_log.cc.o CMakeFiles/ost_img_alg.dir/norm_od.cc.o CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o CMakeFiles/ost_img_alg.dir/randomize.cc.o CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o CMakeFiles/ost_img_alg.dir/stat.cc.o CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o CMakeFiles/ost_img_alg.dir/alg_transform.cc.o CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o CMakeFiles/ost_img_alg.dir/alg_shift.cc.o CMakeFiles/ost_img_alg.dir/threshold.cc.o CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o CMakeFiles/ost_img_alg.dir/transformation_base.cc.o CMakeFiles/ost_img_alg.dir/transformations.cc.o CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o CMakeFiles/ost_img_alg.dir/polar.cc.o CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o CMakeFiles/ost_img_alg.dir/line_average.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3 ../../../../stage/lib/libost_img_alg.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 23%] Built target ost_img_alg [ 24%] Linking CXX shared library ../../../../stage/lib/libost_seq.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_seq.so.2.3 -o ../../../../stage/lib/libost_seq.so.2.3.1 CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o CMakeFiles/ost_seq.dir/sequence_handle.cc.o CMakeFiles/ost_seq.dir/aligned_region.cc.o CMakeFiles/ost_seq.dir/aligned_column.cc.o CMakeFiles/ost_seq.dir/sequence_list.cc.o CMakeFiles/ost_seq.dir/alignment_handle.cc.o CMakeFiles/ost_seq.dir/sequence_op.cc.o CMakeFiles/ost_seq.dir/views_from_sequences.cc.o CMakeFiles/ost_seq.dir/profile_handle.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3 ../../../../stage/lib/libost_seq.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 24%] Built target ost_seq make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings.dir/DependInfo.cmake --color= make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src/CMakeFiles/ost_db.dir/DependInfo.cmake --color= make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -MF CMakeFiles/ost_db.dir/sqlite_wrap.cc.o.d -o CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -c /build/openstructure-2.3.1/modules/db/src/sqlite_wrap.cc make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build [ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/linear_indexer.cc.o make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/linear_indexer.cc.o -MF CMakeFiles/ost_db.dir/linear_indexer.cc.o.d -o CMakeFiles/ost_db.dir/linear_indexer.cc.o -c /build/openstructure-2.3.1/modules/db/src/linear_indexer.cc [ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/extract_data_helper.cc.o [ 24%] Building CXX object modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/extract_data_helper.cc.o -MF CMakeFiles/ost_db.dir/extract_data_helper.cc.o.d -o CMakeFiles/ost_db.dir/extract_data_helper.cc.o -c /build/openstructure-2.3.1/modules/db/src/extract_data_helper.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/c++ -DOST_MODULE_OST_BINDINGS -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_bindings_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -MF CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o.d -o CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -c /build/openstructure-2.3.1/modules/bindings/src/wrap_tmalign.cc [ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/binary_container.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/binary_container.cc.o -MF CMakeFiles/ost_db.dir/binary_container.cc.o.d -o CMakeFiles/ost_db.dir/binary_container.cc.o -c /build/openstructure-2.3.1/modules/db/src/binary_container.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o -MF CMakeFiles/ost_seq_alg.dir/conservation.cc.o.d -o CMakeFiles/ost_seq_alg.dir/conservation.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/conservation.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o -MF CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o.d -o CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/clip_alignment.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -MF CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o.d -o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/contact_prediction_score.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/contact_weight_matrix.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/distance_map.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/distance_map.cc.o -MF CMakeFiles/ost_seq_alg.dir/distance_map.cc.o.d -o CMakeFiles/ost_seq_alg.dir/distance_map.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/distance_map.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/global_align.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/global_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/global_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/global_align.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/global_align.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/entropy.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/entropy.cc.o -MF CMakeFiles/ost_seq_alg.dir/entropy.cc.o.d -o CMakeFiles/ost_seq_alg.dir/entropy.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/entropy.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/ins_del.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/ins_del.cc.o -MF CMakeFiles/ost_seq_alg.dir/ins_del.cc.o.d -o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/ins_del.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/local_align.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/local_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/local_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/local_align.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/local_align.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -MF CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o.d -o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/merge_pairwise_alignments.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/ins_del.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/modules/seq/alg/src/clip_alignment.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/distance_map.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/openstructure-2.3.1/modules/seq/alg/src/conservation.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/distance_map.hh:33, from /build/openstructure-2.3.1/modules/seq/alg/src/distance_map.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:24, from /build/openstructure-2.3.1/modules/db/src/extract_data_helper.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/openstructure-2.3.1/modules/seq/alg/src/contact_prediction_score.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/modules/seq/alg/src/entropy.hh:24, from /build/openstructure-2.3.1/modules/seq/alg/src/entropy.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/modules/seq/alg/src/entropy.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/modules/seq/alg/src/impl/align_impl.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/global_align.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/global_align.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/modules/seq/alg/src/impl/align_impl.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/local_align.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/local_align.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/seq/alg/src/entropy.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/bindings/wrap_tmalign.hh:24, from /build/openstructure-2.3.1/modules/bindings/src/wrap_tmalign.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /build/openstructure-2.3.1/modules/bindings/src/tmalign/param_set.h:6, from /build/openstructure-2.3.1/modules/bindings/src/tmalign/TMalign.h:4, from /build/openstructure-2.3.1/modules/bindings/src/wrap_tmalign.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/semiglobal_align.cc [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o -MF CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o.d -o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/sequence_identity.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/modules/seq/alg/src/merge_pairwise_alignments.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/merge_pairwise_alignments.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/openstructure-2.3.1/modules/seq/alg/src/merge_pairwise_alignments.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/complex:45, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:26: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)' at /build/openstructure-2.3.1/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:27: /usr/include/boost/variant/variant.hpp: In function 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/ios:40: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)' at /build/openstructure-2.3.1/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)' at /build/openstructure-2.3.1/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)' at /build/openstructure-2.3.1/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o -MF CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o.d -o CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/sequence_similarity.cc [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/subst_weight_matrix.cc [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/variance_map.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/variance_map.cc.o -MF CMakeFiles/ost_seq_alg.dir/variance_map.cc.o.d -o CMakeFiles/ost_seq_alg.dir/variance_map.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/variance_map.cc [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o -MF CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o.d -o CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/hmm_pseudo_counts.cc [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -MF CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o.d -o CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/hmm_score.cc [ 25%] Linking CXX shared library ../../../stage/lib/libost_db.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_db.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_db.so.2.3 -o ../../../stage/lib/libost_db.so.2.3.1 CMakeFiles/ost_db.dir/sqlite_wrap.cc.o CMakeFiles/ost_db.dir/linear_indexer.cc.o CMakeFiles/ost_db.dir/binary_container.cc.o CMakeFiles/ost_db.dir/extract_data_helper.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_db.so.2.3.1 ../../../stage/lib/libost_db.so.2.3 ../../../stage/lib/libost_db.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 25%] Built target ost_db make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/processor.cc.o [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/amino_acids.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/processor.cc.o -MF CMakeFiles/ost_conop.dir/processor.cc.o.d -o CMakeFiles/ost_conop.dir/processor.cc.o -c /build/openstructure-2.3.1/modules/conop/src/processor.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/amino_acids.cc.o -MF CMakeFiles/ost_conop.dir/amino_acids.cc.o.d -o CMakeFiles/ost_conop.dir/amino_acids.cc.o -c /build/openstructure-2.3.1/modules/conop/src/amino_acids.cc [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/conop.cc.o [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/conop.cc.o -MF CMakeFiles/ost_conop.dir/conop.cc.o.d -o CMakeFiles/ost_conop.dir/conop.cc.o -c /build/openstructure-2.3.1/modules/conop/src/conop.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o -MF CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o.d -o CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o -c /build/openstructure-2.3.1/modules/conop/src/minimal_compound_lib.cc [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib_base.cc.o -MF CMakeFiles/ost_conop.dir/compound_lib_base.cc.o.d -o CMakeFiles/ost_conop.dir/compound_lib_base.cc.o -c /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/modules/seq/alg/src/impl/align_impl.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/semiglobal_align.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/semiglobal_align.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/heuristic.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/heuristic.cc.o -MF CMakeFiles/ost_conop.dir/heuristic.cc.o.d -o CMakeFiles/ost_conop.dir/heuristic.cc.o -c /build/openstructure-2.3.1/modules/conop/src/heuristic.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/sequence_identity.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/variance_map.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/openstructure-2.3.1/modules/seq/alg/src/variance_map.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/diag.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/diag.cc.o -MF CMakeFiles/ost_conop.dir/diag.cc.o.d -o CMakeFiles/ost_conop.dir/diag.cc.o -c /build/openstructure-2.3.1/modules/conop/src/diag.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/hmm_score.hh:24, from /build/openstructure-2.3.1/modules/seq/alg/src/hmm_score.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/profile_handle.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/hmm_score.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/rule_based.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/rule_based.cc.o -MF CMakeFiles/ost_conop.dir/rule_based.cc.o.d -o CMakeFiles/ost_conop.dir/rule_based.cc.o -c /build/openstructure-2.3.1/modules/conop/src/rule_based.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/conop/src/amino_acids.hh:26, from /build/openstructure-2.3.1/modules/conop/src/amino_acids.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/set:60, from /build/openstructure-2.3.1/modules/conop/src/amino_acids.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/modules/conop/src/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/conop/src/processor.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/conop/src/conop.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/conop/src/conop.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o -MF CMakeFiles/ost_conop.dir/model_check.cc.o.d -o CMakeFiles/ost_conop.dir/model_check.cc.o -c /build/openstructure-2.3.1/modules/conop/src/model_check.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.hh:5, from /build/openstructure-2.3.1/modules/conop/src/minimal_compound_lib.hh:5, from /build/openstructure-2.3.1/modules/conop/src/minimal_compound_lib.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/modules/conop/src/compound.hh:22, from /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.hh:4: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o -MF CMakeFiles/ost_conop.dir/compound.cc.o.d -o CMakeFiles/ost_conop.dir/compound.cc.o -c /build/openstructure-2.3.1/modules/conop/src/compound.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.hh:5, from /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/modules/conop/src/compound.hh:22, from /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.hh:4: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/conop/src/heuristic.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/conop/src/heuristic.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/conop/src/diag.hh:23, from /build/openstructure-2.3.1/modules/conop/src/diag.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, from /build/openstructure-2.3.1/modules/conop/src/diag.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o -MF CMakeFiles/ost_conop.dir/compound_lib.cc.o.d -o CMakeFiles/ost_conop.dir/compound_lib.cc.o -c /build/openstructure-2.3.1/modules/conop/src/compound_lib.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/conop/src/rule_based.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/conop/src/rule_based.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/ring_finder.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/ring_finder.cc.o -MF CMakeFiles/ost_conop.dir/ring_finder.cc.o.d -o CMakeFiles/ost_conop.dir/ring_finder.cc.o -c /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/modules/conop/src/model_check.hh:4, from /build/openstructure-2.3.1/modules/conop/src/model_check.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/conop/src/model_check.cc:2: /build/openstructure-2.3.1/modules/conop/src/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.hh:5, from /build/openstructure-2.3.1/modules/conop/src/compound_lib.hh:27, from /build/openstructure-2.3.1/modules/conop/src/compound_lib.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/conop/src/compound_lib.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/complex:45, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:24: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/ios:40: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:93:21: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:93:21: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:93:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:93:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:121:23: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:121:23: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:121:23: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:121:23: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 26%] Linking CXX shared library ../../../stage/lib/libost_bindings.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_bindings.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_bindings.so.2.3 -o ../../../stage/lib/libost_bindings.so.2.3.1 CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_bindings.so.2.3.1 ../../../stage/lib/libost_bindings.so.2.3 ../../../stage/lib/libost_bindings.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 26%] Built target ost_bindings [ 26%] Linking CXX shared library ../../../../stage/lib/libost_seq_alg.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_seq_alg.so.2.3 -o ../../../../stage/lib/libost_seq_alg.so.2.3.1 CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o CMakeFiles/ost_seq_alg.dir/conservation.cc.o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/distance_map.cc.o CMakeFiles/ost_seq_alg.dir/entropy.cc.o CMakeFiles/ost_seq_alg.dir/global_align.cc.o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o CMakeFiles/ost_seq_alg.dir/local_align.cc.o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/variance_map.cc.o CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_seq_alg.so.2.3 ../../../../stage/lib/libost_seq_alg.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 26%] Built target ost_seq_alg [ 26%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/info/_ost_info.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_info.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/info/_ost_info.so CMakeFiles/_ost_info.dir/wrap_info.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/info/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/info/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 26%] Built target _ost_info make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/depend make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom.cc.o -MF CMakeFiles/_ost_mol.dir/export_atom.cc.o.d -o CMakeFiles/_ost_mol.dir/export_atom.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom.cc [ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom_view.cc.o [ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_atom_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_atom_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom_view.cc [ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o [ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o -MF CMakeFiles/_ost_mol.dir/export_bond.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bond.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_bond.cc [ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o -MF CMakeFiles/_ost_img.dir/export_data.cc.o.d -o CMakeFiles/_ost_img.dir/export_data.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_data.cc [ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o -MF CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o.d -o CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_data_algorithm.cc [ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain.cc [ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain_view.cc [ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_handle.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o -MF CMakeFiles/_ost_img.dir/export_extent.cc.o.d -o CMakeFiles/_ost_img.dir/export_extent.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_extent.cc [ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_group.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_group.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_handle.cc.o -MF CMakeFiles/_ost_img.dir/export_image_handle.cc.o.d -o CMakeFiles/_ost_img.dir/export_image_handle.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_image_handle.cc [ 28%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_frame.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o -MF CMakeFiles/_ost_img.dir/export_peak.cc.o.d -o CMakeFiles/_ost_img.dir/export_peak.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_peak.cc [ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o [ 28%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o -MF CMakeFiles/_ost_img.dir/export_phase.cc.o.d -o CMakeFiles/_ost_img.dir/export_phase.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_phase.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o -MF CMakeFiles/_ost_mol.dir/export_editors.cc.o.d -o CMakeFiles/_ost_mol.dir/export_editors.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_frame.cc:24: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_frame.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/base/pymod/export_image_handle.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom_view.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/base/pymod/export_phase.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_group.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/base/pymod/export_extent.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain_view.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/base/pymod/export_data_algorithm.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/base/pymod/export_peak.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_bond.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/base/pymod/export_image_handle.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/pymod/wrap_extent_iterator.hh:34, from /build/openstructure-2.3.1/modules/img/base/pymod/export_extent.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/base/pymod/export_data.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom_view.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_group.hh:29, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_group.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain_view.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/base/pymod/export_data_algorithm.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/peak.hh:31, from /build/openstructure-2.3.1/modules/img/base/pymod/export_peak.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_bond.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/modules/img/base/pymod/export_data.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o -MF CMakeFiles/_ost_img.dir/export_point.cc.o.d -o CMakeFiles/_ost_img.dir/export_point.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_point.cc [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc [ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o -MF CMakeFiles/_ost_img.dir/export_progress.cc.o.d -o CMakeFiles/_ost_img.dir/export_progress.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_progress.cc [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_view.cc [ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o -MF CMakeFiles/_ost_img.dir/export_raster_image.cc.o.d -o CMakeFiles/_ost_img.dir/export_raster_image.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_raster_image.cc [ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o -MF CMakeFiles/_ost_img.dir/export_size.cc.o.d -o CMakeFiles/_ost_img.dir/export_size.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_size.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/base/pymod/export_point.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point_list.hh:28, from /build/openstructure-2.3.1/modules/img/base/pymod/export_point.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o -MF CMakeFiles/_ost_mol.dir/export_property_id.cc.o.d -o CMakeFiles/_ost_mol.dir/export_property_id.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_property_id.cc [ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o -MF CMakeFiles/_ost_img.dir/export_mask.cc.o.d -o CMakeFiles/_ost_img.dir/export_mask.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_mask.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/base/pymod/export_progress.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/base/pymod/export_size.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_view.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o -MF CMakeFiles/_ost_img.dir/export_image_list.cc.o.d -o CMakeFiles/_ost_img.dir/export_image_list.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_image_list.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/pymod/export_size.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/base/pymod/export_raster_image.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o -MF CMakeFiles/_ost_mol.dir/export_query.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_query.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_view.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh:31, from /build/openstructure-2.3.1/modules/img/base/pymod/export_raster_image.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_property_id.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o -MF CMakeFiles/_ost_img.dir/export_map.cc.o.d -o CMakeFiles/_ost_img.dir/export_map.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/export_map.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_property_id.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/base/pymod/export_mask.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.cc.o -MF CMakeFiles/_ost_img.dir/wrap_img.cc.o.d -o CMakeFiles/_ost_img.dir/wrap_img.cc.o -c /build/openstructure-2.3.1/modules/img/base/pymod/wrap_img.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/polygon_mask.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/mask.hh:29, from /build/openstructure-2.3.1/modules/img/base/pymod/export_mask.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue_view.cc [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o -MF CMakeFiles/_ost_mol.dir/export_surface.cc.o.d -o CMakeFiles/_ost_mol.dir/export_surface.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_surface.cc [ 29%] Linking CXX shared library ../../../stage/lib/libost_conop.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_conop.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_conop.so.2.3 -o ../../../stage/lib/libost_conop.so.2.3.1 CMakeFiles/ost_conop.dir/processor.cc.o CMakeFiles/ost_conop.dir/amino_acids.cc.o CMakeFiles/ost_conop.dir/conop.cc.o CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o CMakeFiles/ost_conop.dir/compound_lib_base.cc.o CMakeFiles/ost_conop.dir/heuristic.cc.o CMakeFiles/ost_conop.dir/diag.cc.o CMakeFiles/ost_conop.dir/rule_based.cc.o CMakeFiles/ost_conop.dir/model_check.cc.o CMakeFiles/ost_conop.dir/compound.cc.o CMakeFiles/ost_conop.dir/compound_lib.cc.o CMakeFiles/ost_conop.dir/ring_finder.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/base/pymod/export_image_list.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_query.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3 ../../../stage/lib/libost_conop.so [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -MF CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_bounding_box.cc make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 29%] Built target ost_conop [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_query_view_wrapper.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/base/pymod/export_image_list.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_query.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o -MF CMakeFiles/_ost_mol.dir/export_torsion.cc.o.d -o CMakeFiles/_ost_mol.dir/export_torsion.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_torsion.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/base/pymod/export_map.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o -MF CMakeFiles/_ost_mol.dir/export_visitor.cc.o.d -o CMakeFiles/_ost_mol.dir/export_visitor.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_visitor.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/openstructure-2.3.1/modules/img/base/pymod/export_map.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -MF CMakeFiles/_ost_mol.dir/wrap_mol.cc.o.d -o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/wrap_mol.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/base/pymod/wrap_img.cc:27: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/base/pymod/wrap_img.cc:33: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_surface.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue_view.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_property_mapper.cc make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -MF CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o.d -o CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -MF CMakeFiles/ost_gfx.dir/bitmap_io.cc.o.d -o CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/bitmap_io.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_surface.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_bounding_box.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_query_view_wrapper.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue_view.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o -MF CMakeFiles/ost_gfx.dir/exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/exporter.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/exporter.cc In file included from /usr/include/boost/bind.hpp:30, from /build/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc:22: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_bounding_box.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_query_view_wrapper.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_torsion.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_visitor.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, from /build/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/collada_exporter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/collada_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/collada_exporter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/exporter.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_visitor.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color.cc.o -MF CMakeFiles/ost_gfx.dir/color.cc.o.d -o CMakeFiles/ost_gfx.dir/color.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/wrap_mol.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_property_mapper.cc:1: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/primitives.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/primitives.cc.o -MF CMakeFiles/ost_gfx.dir/primitives.cc.o.d -o CMakeFiles/ost_gfx.dir/primitives.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/primitives.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/editor_base.hh:27, from /build/openstructure-2.3.1/modules/mol/base/pymod/wrap_mol.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_property_mapper.cc:3: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 32%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/img/_ost_img.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/img/_ost_img.so CMakeFiles/_ost_img.dir/export_data.cc.o CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o CMakeFiles/_ost_img.dir/export_extent.cc.o CMakeFiles/_ost_img.dir/export_image_handle.cc.o CMakeFiles/_ost_img.dir/export_peak.cc.o CMakeFiles/_ost_img.dir/export_phase.cc.o CMakeFiles/_ost_img.dir/export_point.cc.o CMakeFiles/_ost_img.dir/export_progress.cc.o CMakeFiles/_ost_img.dir/export_raster_image.cc.o CMakeFiles/_ost_img.dir/export_size.cc.o CMakeFiles/_ost_img.dir/export_mask.cc.o CMakeFiles/_ost_img.dir/export_image_list.cc.o CMakeFiles/_ost_img.dir/export_map.cc.o CMakeFiles/_ost_img.dir/wrap_img.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/collada_exporter.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/openstructure-2.3.1/modules/gfx/src/collada_exporter.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/color.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/modules/gfx/src/color.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/img/base/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 32%] Built target _ost_img make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 33%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -MF CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o.d -o CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -c /build/openstructure-2.3.1/modules/img/alg/pymod/wrap_alg.cc [ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.cc.o -MF CMakeFiles/ost_gfx.dir/entity.cc.o.d -o CMakeFiles/ost_gfx.dir/entity.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/entity.cc [ 33%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_filter.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -c /build/openstructure-2.3.1/modules/img/alg/pymod/export_filter.cc [ 33%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -c /build/openstructure-2.3.1/modules/img/alg/pymod/export_normalizer.cc [ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -MF CMakeFiles/ost_gfx.dir/symmetry_node.cc.o.d -o CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/symmetry_node.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/primitives.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/primitives.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/gl_helper.hh:36, from /build/openstructure-2.3.1/modules/gfx/src/primitives.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_node.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_node.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gfx_node.cc [ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_object.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gfx_object.cc [ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_prim.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gfx_prim.cc [ 33%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -c /build/openstructure-2.3.1/modules/img/alg/pymod/export_transcendentals.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/symmetry_node.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/symmetry_node.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/gl_helper.hh:36, from /build/openstructure-2.3.1/modules/gfx/src/symmetry_node.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/modules/gfx/src/entity.cc:36: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/gfx/src/entity.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/openstructure-2.3.1/modules/gfx/src/gfx_node.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/gfx_prim.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/gfx_prim.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/modules/gfx/src/gfx_prim.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gfx_test_object.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/alg/pymod/export_filter.cc:27: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o -MF CMakeFiles/ost_gfx.dir/input.cc.o.d -o CMakeFiles/ost_gfx.dir/input.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/input.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/gfx_object_base.hh:26, from /build/openstructure-2.3.1/modules/gfx/src/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gfx/src/gfx_node.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/config/no_tr1/memory.hpp:21, from /usr/include/boost/get_pointer.hpp:14, from /usr/include/boost/bind/mem_fn.hpp:25, from /usr/include/boost/mem_fn.hpp:22, from /usr/include/boost/bind/bind.hpp:26, from /usr/include/boost/bind.hpp:29: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/alg/pymod/wrap_alg.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/gfx_object.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/gfx_object.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 33%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_polar.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -c /build/openstructure-2.3.1/modules/img/alg/pymod/export_polar.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/alg/pymod/export_normalizer.cc:27: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/gaussian.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/filter.hh:30, from /build/openstructure-2.3.1/modules/img/alg/pymod/export_filter.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o -MF CMakeFiles/ost_gfx.dir/prim_list.cc.o.d -o CMakeFiles/ost_gfx.dir/prim_list.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/prim_list.cc [ 33%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -MF CMakeFiles/ost_mol_alg.dir/clash_score.cc.o.d -o CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/clash_score.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/auto_correlate.hh:24, from /build/openstructure-2.3.1/modules/img/alg/pymod/wrap_alg.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 33%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/sec_structure_segments.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, from /build/openstructure-2.3.1/modules/img/alg/pymod/export_normalizer.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/alg/pymod/export_transcendentals.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/gfx_object_base.hh:26, from /build/openstructure-2.3.1/modules/gfx/src/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gfx/src/gfx_test_object.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/gfx_test_object.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/boost/system/error_code.hpp:17, from /usr/include/boost/filesystem/path_traits.hpp:22, from /usr/include/boost/filesystem/path.hpp:26, from /usr/include/boost/filesystem/operations.hpp:26, from /build/openstructure-2.3.1/modules/gfx/src/gfx_test_object.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/transcendentals.hh:34, from /build/openstructure-2.3.1/modules/img/alg/pymod/export_transcendentals.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/sec_structure_segments.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/alg/src/clash_score.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/prim_list.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/prim_list.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 33%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.cc.o -MF CMakeFiles/ost_gfx.dir/scene.cc.o.d -o CMakeFiles/ost_gfx.dir/scene.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/scene.cc [ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/distance_test_common.cc [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/selection.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/selection.cc.o -MF CMakeFiles/ost_gfx.dir/selection.cc.o.d -o CMakeFiles/ost_gfx.dir/selection.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/selection.cc [ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/img/alg/pymod/export_polar.cc:24: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.cc.o -MF CMakeFiles/ost_gfx.dir/surface.cc.o.d -o CMakeFiles/ost_gfx.dir/surface.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/surface.cc [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient.cc.o -MF CMakeFiles/ost_gfx.dir/gradient.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gradient.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/polar.hh:24, from /build/openstructure-2.3.1/modules/img/alg/pymod/export_polar.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.cc.o -MF CMakeFiles/ost_gfx.dir/gradient_manager.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient_manager.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gradient_manager.cc In file included from /usr/include/boost/bind.hpp:30, from /build/openstructure-2.3.1/modules/gfx/src/scene.cc:33: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc:4: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/iomanip:40, from /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.hh:24, from /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc:6: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/distance_test_common.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/distance_test_common.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/selection.hh:26, from /build/openstructure-2.3.1/modules/gfx/src/selection.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/scene.cc:40: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/scene.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:2: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/distance_rmsd_test.hh:24, from /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:3: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/vertex_array_helper.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/gradient.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/gradient.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/modules/gfx/src/gradient.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o -MF CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o.d -o CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/superpose_frames.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/gfx/src/gradient_manager.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/boost/system/error_code.hpp:17, from /usr/include/boost/filesystem/path_traits.hpp:22, from /usr/include/boost/filesystem/path.hpp:26, from /usr/include/boost/filesystem/operations.hpp:26, from /build/openstructure-2.3.1/modules/gfx/src/gradient_manager.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/material.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/material.cc.o -MF CMakeFiles/ost_gfx.dir/material.cc.o.d -o CMakeFiles/ost_gfx.dir/material.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/material.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/surface.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/openstructure-2.3.1/modules/gfx/src/surface.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.cc.o -MF CMakeFiles/ost_gfx.dir/povray.cc.o.d -o CMakeFiles/ost_gfx.dir/povray.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/povray.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/vertex_array_helper.hh:23, from /build/openstructure-2.3.1/modules/gfx/src/vertex_array_helper.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/modules/gfx/src/vertex_array_helper.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -MF CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o.d -o CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/filter_clashes.cc [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/gost_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/gost_exporter.cc [ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -MF CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o.d -o CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/construct_cbeta.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/material.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/material.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/iterator:61, from /usr/include/boost/operators.hpp:98, from /build/openstructure-2.3.1/modules/gfx/src/color.hh:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/vertex_array.hh:34, from /build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /usr/include/boost/format.hpp:17, from /build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/povray.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/povray.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/openstructure-2.3.1/modules/gfx/src/povray.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/texture.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/texture.cc.o -MF CMakeFiles/ost_gfx.dir/texture.cc.o.d -o CMakeFiles/ost_gfx.dir/texture.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/texture.cc [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/filter_clashes.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/filter_clashes.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/construct_cbeta.cc:4: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/mol/alg/src/construct_cbeta.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/superpose_frames.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/eigen3/Eigen/src/Core/util/Macros.h:679, from /usr/include/eigen3/Eigen/Core:19, from /usr/include/eigen3/Eigen/Eigenvalues:11, from /build/openstructure-2.3.1/modules/mol/alg/src/superpose_frames.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.cc /build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:1311:8: warning: 'geom::Vec3 ost::gfx::{anonymous}::make_aaline_edge(const geom::Vec2&, const geom::Vec2&, float)' defined but not used [-Wunused-function] 1311 | Vec3 make_aaline_edge(const Vec2& c1, const Vec2& c0, float s) | ^~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:1239:8: warning: 'void ost::gfx::{anonymous}::render_aalines(AALineList&, float, float)' defined but not used [-Wunused-function] 1239 | void render_aalines(AALineList& line_list, float w, float r) | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:53: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/ios:40: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/gost_exporter.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/openstructure-2.3.1/modules/gfx/src/gost_exporter.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/trajectory_analysis.cc [ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/structure_analysis.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.hh:24, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.hh:23, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.cc [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.cc [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/alg/src/trajectory_analysis.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/modules/mol/alg/src/trajectory_analysis.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/dyn_cast.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/structure_analysis.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/structure_analysis.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -MF CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o.d -o CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/consistency_checks.cc [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_handle.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -MF CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.cc [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o [ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -MF CMakeFiles/ost_mol_alg.dir/pdbize.cc.o.d -o CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/pdbize.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/dyn_cast.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/modules/mol/alg/src/consistency_checks.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/consistency_checks.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -MF CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o.d -o CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.cc [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.cc [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_op.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, from /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.cc [ 38%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/mol/_ost_mol.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/mol/_ost_mol.so CMakeFiles/_ost_mol.dir/export_atom.cc.o CMakeFiles/_ost_mol.dir/export_atom_view.cc.o CMakeFiles/_ost_mol.dir/export_bond.cc.o CMakeFiles/_ost_mol.dir/export_chain.cc.o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o CMakeFiles/_ost_mol.dir/export_editors.cc.o CMakeFiles/_ost_mol.dir/export_entity.cc.o CMakeFiles/_ost_mol.dir/export_entity_view.cc.o CMakeFiles/_ost_mol.dir/export_property_id.cc.o CMakeFiles/_ost_mol.dir/export_query.cc.o CMakeFiles/_ost_mol.dir/export_residue.cc.o CMakeFiles/_ost_mol.dir/export_residue_view.cc.o CMakeFiles/_ost_mol.dir/export_surface.cc.o CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o CMakeFiles/_ost_mol.dir/export_torsion.cc.o CMakeFiles/_ost_mol.dir/export_visitor.cc.o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/alg/src/pdbize.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/pdbize.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/mol/alg/src/pdbize.hh:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o [ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -MF CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o.d -o CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_view.hh:25, from /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.hh:27, from /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -MF CMakeFiles/ost_mol_alg.dir/domain_find.cc.o.d -o CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.hh:32, from /build/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/base/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/./__init__.pyc\",\"__init__.py\",doraise=True)" [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.cc make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 38%] Built target _ost_mol make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/DependInfo.cmake --color= In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.hh:9, from /build/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 38%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_sequence.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_sequence.cc.o -MF CMakeFiles/_ost_seq.dir/export_sequence.cc.o.d -o CMakeFiles/_ost_seq.dir/export_sequence.cc.o -c /build/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:23, from /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, from /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh:24, from /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:2: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -MF CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o.d -o CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:3: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:27, from /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/img/alg/_ost_img_alg.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/img/alg/_ost_img_alg.so CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, from /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/img/alg/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 38%] Built target _ost_img_alg In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, from /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity_fw.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -MF CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.cc [ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/accessibility.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -MF CMakeFiles/ost_mol_alg.dir/accessibility.cc.o.d -o CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.hh:7, from /build/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.hh:5: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/sec_struct.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, from /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o -MF CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.cc [ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -MF CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o.d -o CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/nonstandard.cc [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o -MF CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.hh:32, from /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:3: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/thread/exceptions.hpp:20, from /usr/include/boost/thread/pthread/thread_data.hpp:10, from /usr/include/boost/thread/thread_only.hpp:17, from /usr/include/boost/thread/thread.hpp:12, from /usr/include/boost/thread.hpp:13, from /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o -MF CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:9: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -MF CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/tabulated_trig.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, from /build/openstructure-2.3.1/modules/mol/alg/src/sec_struct.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, from /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:53: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/ios:40: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:34: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:37: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/mol/alg/src/nonstandard.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/line_render_options.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o -MF CMakeFiles/ost_mol_alg.dir/molck.cc.o.d -o CMakeFiles/ost_mol_alg.dir/molck.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/molck.cc [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/custom_render_options.cc [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/cpk_render_options.cc [ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -MF CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o.d -o CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/input.hh:30, from /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -MF CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o.d -o CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/src/entity_to_density.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/mol/alg/src/molck.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/sline_render_options.cc [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/line_trace_render_options.cc [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/render_options/cartoon_render_options.cc In file included from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/complex:45, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:24: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_base.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:27: /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/ios:40: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /build/openstructure-2.3.1/modules/mol/alg/src/molck.cc:4: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.cc.o -MF CMakeFiles/ost_gfx.dir/map_iso.cc.o.d -o CMakeFiles/ost_gfx.dir/map_iso.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/map_iso.cc [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_slab.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/map_slab.cc.o -MF CMakeFiles/ost_gfx.dir/map_slab.cc.o.d -o CMakeFiles/ost_gfx.dir/map_slab.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/map_slab.cc [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.cc [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.cc In file included from /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:11: In member function 'void ost::mol::alg::AdjacencyBitmap::set(size_t, size_t, bool, bool)', inlined from 'ost::mol::alg::AdjacencyBitmap::AdjacencyBitmap(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, int, int)' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:49:16, inlined from 'static ost::mol::alg::DomainsPtr ost::mol::alg::Domains::FromDistMats(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, Real, int, bool, bool)' at /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:363:37: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:109:23: warning: 'malloc' may be used uninitialized [-Wmaybe-uninitialized] 109 | data_[byte_index] &= ~(one << bit_index); | ~~~~~~~~~~~~~~~~^ [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_o.cc [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.cc [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -MF CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -c /build/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/dft.hh:24, from /build/openstructure-2.3.1/modules/mol/alg/src/entity_to_density.cc:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/openstructure-2.3.1/modules/mol/alg/src/entity_to_density.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 42%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -MF CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o.d -o CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -c /build/openstructure-2.3.1/modules/seq/base/pymod/export_profile_handle.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/discrete_shrink.hh:24, from /build/openstructure-2.3.1/modules/gfx/src/map_iso.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/map_iso.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/vertex_array.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_iso_prop.hh:26, from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_o.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/shared_array.hpp:19, from /usr/include/boost/shared_array.hpp:17, from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_o.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, from /build/openstructure-2.3.1/modules/gfx/src/map_slab.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/modules/gfx/src/map_slab.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:32: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/QR:11, from /usr/include/eigen3/Eigen/SVD:11, from /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.cc:26: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const float*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/shared_array.hpp:19, from /usr/include/boost/shared_array.hpp:17, from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:27, from /build/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_construct.h:61, from /usr/include/c++/12/bits/alloc_traits.h:33, from /usr/include/c++/12/ext/alloc_traits.h:34, from /usr/include/c++/12/unordered_map:41, from /usr/include/c++/12/functional:61, from /usr/include/boost/container_hash/hash.hpp:20, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_map.hpp:18, from /usr/include/boost/unordered_map.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 42%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -MF CMakeFiles/_ost_seq.dir/wrap_seq.cc.o.d -o CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -c /build/openstructure-2.3.1/modules/seq/base/pymod/wrap_seq.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object/class.hpp:9, from /usr/include/boost/python/class.hpp:13, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:9, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /build/openstructure-2.3.1/modules/seq/base/pymod/export_profile_handle.cc:24: /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/seq/base/pymod/wrap_seq.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/complex:45, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:24: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)' at /build/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In function 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/ios:40: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)' at /build/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)' at /build/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)' at /build/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 42%] Linking CXX shared library ../../../../stage/lib/libost_mol_alg.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/atom_scattering_properties.txt /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/atom_scattering_properties.txt cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/stereo_chemical_props.txt /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/stereo_chemical_props.txt cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol_alg.so.2.3 -o ../../../../stage/lib/libost_mol_alg.so.2.3.1 CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o CMakeFiles/ost_mol_alg.dir/clash_score.cc.o CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o CMakeFiles/ost_mol_alg.dir/pdbize.cc.o CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o CMakeFiles/ost_mol_alg.dir/domain_find.cc.o CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o CMakeFiles/ost_mol_alg.dir/accessibility.cc.o CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o CMakeFiles/ost_mol_alg.dir/molck.cc.o CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libsqlite3.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3 ../../../../stage/lib/libost_mol_alg.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 42%] Built target ost_mol_alg make -f modules/io/src/CMakeFiles/ost_io.dir/build.make modules/io/src/CMakeFiles/ost_io.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src/CMakeFiles/ost_io.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/io/src/CMakeFiles/ost_io.dir/build.make modules/io/src/CMakeFiles/ost_io.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_manager.cc.o [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/convert.cc.o [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_utils.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/io_manager.cc.o -MF CMakeFiles/ost_io.dir/io_manager.cc.o.d -o CMakeFiles/ost_io.dir/io_manager.cc.o -c /build/openstructure-2.3.1/modules/io/src/io_manager.cc [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/convert.cc.o -MF CMakeFiles/ost_io.dir/convert.cc.o.d -o CMakeFiles/ost_io.dir/convert.cc.o -c /build/openstructure-2.3.1/modules/io/src/convert.cc [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/io_utils.cc.o -MF CMakeFiles/ost_io.dir/io_utils.cc.o.d -o CMakeFiles/ost_io.dir/io_utils.cc.o -c /build/openstructure-2.3.1/modules/io/src/io_utils.cc [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/pdb_writer.cc [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.cc [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.cc [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.cc [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o -MF CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o.d -o CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.cc [ 43%] Linking CXX shared library ../../../stage/lib/libost_gfx.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/test_texture.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/textures/test_texture.png cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/glyph_texture.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/textures/glyph_texture.png cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gfx.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_gfx.so.2.3 -o ../../../stage/lib/libost_gfx.so.2.3.1 CMakeFiles/ost_gfx.dir/bitmap_io.cc.o CMakeFiles/ost_gfx.dir/exporter.cc.o CMakeFiles/ost_gfx.dir/collada_exporter.cc.o CMakeFiles/ost_gfx.dir/color.cc.o CMakeFiles/ost_gfx.dir/primitives.cc.o CMakeFiles/ost_gfx.dir/entity.cc.o CMakeFiles/ost_gfx.dir/symmetry_node.cc.o CMakeFiles/ost_gfx.dir/gfx_node.cc.o CMakeFiles/ost_gfx.dir/gfx_object.cc.o CMakeFiles/ost_gfx.dir/gfx_prim.cc.o CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o CMakeFiles/ost_gfx.dir/input.cc.o CMakeFiles/ost_gfx.dir/prim_list.cc.o CMakeFiles/ost_gfx.dir/scene.cc.o CMakeFiles/ost_gfx.dir/selection.cc.o CMakeFiles/ost_gfx.dir/surface.cc.o CMakeFiles/ost_gfx.dir/gradient.cc.o CMakeFiles/ost_gfx.dir/gradient_manager.cc.o CMakeFiles/ost_gfx.dir/vertex_array.cc.o CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o CMakeFiles/ost_gfx.dir/material.cc.o CMakeFiles/ost_gfx.dir/povray.cc.o CMakeFiles/ost_gfx.dir/gost_exporter.cc.o CMakeFiles/ost_gfx.dir/texture.cc.o CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o CMakeFiles/ost_gfx.dir/map_iso.cc.o CMakeFiles/ost_gfx.dir/map_slab.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so ../../../stage/lib/libost_db.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/save_entity.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/save_entity.cc.o -MF CMakeFiles/ost_io.dir/mol/save_entity.cc.o.d -o CMakeFiles/ost_io.dir/mol/save_entity.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/save_entity.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/src/io_manager.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/load_entity.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/load_entity.cc.o -MF CMakeFiles/ost_io.dir/mol/load_entity.cc.o.d -o CMakeFiles/ost_io.dir/mol/load_entity.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/load_entity.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_gfx.so.2.3.1 ../../../stage/lib/libost_gfx.so.2.3 ../../../stage/lib/libost_gfx.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 43%] Built target ost_gfx [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh:35, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_writer.cc:35: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/locale:39, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_writer.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.cc:35: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.cc:33: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.cc:35: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/algorithm/string/std/string_traits.hpp:15, from /usr/include/boost/algorithm/string/std_containers_traits.hpp:19, from /usr/include/boost/algorithm/string.hpp:18, from /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /usr/include/boost/iostreams/filter/gzip.hpp:21, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.cc:35: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/src/mol/save_entity.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/io/src/mol/save_entity.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.cc:38: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc:34: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface.hh:22, from /build/openstructure-2.3.1/modules/io/src/mol/surface_io_handler.hh:25, from /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.hh:22, from /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/load_surface.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/load_surface.cc.o -MF CMakeFiles/ost_io.dir/mol/load_surface.cc.o.d -o CMakeFiles/ost_io.dir/mol/load_surface.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/load_surface.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh:35, from /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/load_entity.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/io/src/mol/load_entity.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/src/mol/load_entity.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/format/alt_sstream.hpp:22, from /usr/include/boost/format/internals.hpp:24, from /usr/include/boost/format.hpp:38, from /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh:33: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -MF CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o.d -o CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.cc [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/io_profile.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/io_profile.cc.o -MF CMakeFiles/ost_io.dir/mol/io_profile.cc.o.d -o CMakeFiles/ost_io.dir/mol/io_profile.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/io_profile.cc [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -MF CMakeFiles/ost_io.dir/mol/dcd_io.cc.o.d -o CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/load_surface.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/io/src/mol/load_surface.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/src/mol/load_surface.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/star_parser.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/star_parser.cc.o -MF CMakeFiles/ost_io.dir/mol/star_parser.cc.o.d -o CMakeFiles/ost_io.dir/mol/star_parser.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/star_parser.cc [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/modules/io/src/mol/io_profile.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/io_profile.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/io/src/mol/io_profile.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:30, from /build/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.cc:1: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chem_class.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.cc:33: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o -MF CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o.d -o CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.cc:40: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_str.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_str.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_str.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_str.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.cc [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.cc [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o -MF CMakeFiles/ost_io.dir/mol/omf.cc.o.d -o CMakeFiles/ost_io.dir/mol/omf.cc.o -c /build/openstructure-2.3.1/modules/io/src/mol/omf.cc [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh:25, from /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_exception.hh:22, from /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/profile.hh:22, from /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/load.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/load.cc.o -MF CMakeFiles/ost_io.dir/seq/load.cc.o.d -o CMakeFiles/ost_io.dir/seq/load.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/load.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25, from /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh:23, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/stereochemical_params_reader.hh:23, from /build/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/boost/system/error_code.hpp:17, from /usr/include/boost/filesystem/path_traits.hpp:22, from /usr/include/boost/filesystem/path.hpp:26, from /usr/include/boost/filesystem/fstream.hpp:21, from /build/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/save.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/save.cc.o -MF CMakeFiles/ost_io.dir/seq/save.cc.o.d -o CMakeFiles/ost_io.dir/seq/save.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/save.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/io/src/mol/omf.cc:2: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, from /build/openstructure-2.3.1/modules/io/src/mol/omf.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/io/src/seq/load.hh:27, from /build/openstructure-2.3.1/modules/io/src/seq/load.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/module_config.hh:22, from /build/openstructure-2.3.1/modules/io/src/seq/load.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mmcif_info.hh:25, from /build/openstructure-2.3.1/modules/io/src/mol/omf.hh:29, from /build/openstructure-2.3.1/modules/io/src/mol/omf.cc:6: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.hh:25, from /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.cc [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/hhm_io_handler.cc [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/seq/pssm_io_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/src/seq/save.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/openstructure-2.3.1/modules/io/src/seq/save.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 47%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/seq/_ost_seq.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_seq.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/seq/_ost_seq.so CMakeFiles/_ost_seq.dir/export_sequence.cc.o CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh:25, from /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/module_config.hh:22, from /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/load_map.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/load_map.cc.o -MF CMakeFiles/ost_io.dir/img/load_map.cc.o.d -o CMakeFiles/ost_io.dir/img/load_map.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/load_map.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/base/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 47%] Built target _ost_seq make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/depend In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 47%] Building CXX object modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_bindings_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o -MF CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o.d -o CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o -c /build/openstructure-2.3.1/modules/bindings/pymod/export_tmalign.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh:25, from /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/module_config.hh:22, from /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.cc [ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.cc [ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.hh:26, from /build/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/openstructure-2.3.1/modules/io/src/img/load_map.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/io/src/img/load_map.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/src/img/load_map.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.cc:35: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:32: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.cc:37: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.cc:34: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/iomanip:40, from /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:34: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.cc:37: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/bindings/pymod/export_tmalign.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:43: /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:51:40: warning: 'int32' is deprecated [-Wdeprecated-declarations] 51 | class complexint32:public std::complex{ | ^~~~~ In file included from /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:24: /usr/include/x86_64-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:61:40: warning: 'int16' is deprecated [-Wdeprecated-declarations] 61 | class complexint16:public std::complex{ | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:71:39: warning: 'int8' is deprecated [-Wdeprecated-declarations] 71 | class complexint8:public std::complex{ | ^~~~ /usr/include/x86_64-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:105:114: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 105 | void do_tiff_read(tdata_t buf,unsigned int rps, unsigned int width, IST* is,unsigned int& current_row, uint16 spp) | ^ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc: In member function 'virtual void ost::io::MapIOTiffHandler::do_export(const ost::img::MapHandle&, TIFF*, ost::io::TIF&) const': /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:310:10: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 310 | uint16 spp=1; | ^~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:311:10: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 311 | uint16 fmt =0; | ^~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:312:10: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 312 | uint16 bpp =0 ; | ^~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:338:40: warning: 'int8' is deprecated [-Wdeprecated-declarations] 338 | fsr=detail::do_tiff_write; | ^~~~ /usr/include/x86_64-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:343:40: warning: 'int16' is deprecated [-Wdeprecated-declarations] 343 | fsr=detail::do_tiff_write; | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:348:40: warning: 'int32' is deprecated [-Wdeprecated-declarations] 348 | fsr=detail::do_tiff_write; | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:363:40: warning: 'int16' is deprecated [-Wdeprecated-declarations] 363 | fsr=detail::do_tiff_write; | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:371:40: warning: 'uint8' is deprecated [-Wdeprecated-declarations] 371 | fsr=detail::do_tiff_write; | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:80:37: note: declared here 80 | typedef TIFF_MSC_DEPRECATED uint8_t uint8 TIFF_GCC_DEPRECATED; | ^~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:376:40: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 376 | fsr=detail::do_tiff_write; | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:381:40: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 381 | fsr=detail::do_tiff_write; | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:396:40: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 396 | fsr=detail::do_tiff_write; | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:406:54: warning: 'int8' is deprecated [-Wdeprecated-declarations] 406 | fsc=detail::do_tiff_write,img::image_state::ComplexSpatialImageState>; | ^~~~ /usr/include/x86_64-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:411:54: warning: 'int16' is deprecated [-Wdeprecated-declarations] 411 | fsc=detail::do_tiff_write,img::image_state::ComplexSpatialImageState>; | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:416:54: warning: 'int32' is deprecated [-Wdeprecated-declarations] 416 | fsc=detail::do_tiff_write,img::image_state::ComplexSpatialImageState>; | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc: In member function 'void ost::io::MapIOTiffHandler::load_image_data(TIFF*, ost::img::ImageHandle&, const ost::io::TIF&)': /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:556:10: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 556 | uint16 bpp,spp,plc,ori,reso=RESUNIT_NONE,fmt=SAMPLEFORMAT_UINT; | ^~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:556:14: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 556 | uint16 bpp,spp,plc,ori,reso=RESUNIT_NONE,fmt=SAMPLEFORMAT_UINT; | ^~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:556:18: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 556 | uint16 bpp,spp,plc,ori,reso=RESUNIT_NONE,fmt=SAMPLEFORMAT_UINT; | ^~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:556:22: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 556 | uint16 bpp,spp,plc,ori,reso=RESUNIT_NONE,fmt=SAMPLEFORMAT_UINT; | ^~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:556:26: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 556 | uint16 bpp,spp,plc,ori,reso=RESUNIT_NONE,fmt=SAMPLEFORMAT_UINT; | ^~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:556:44: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 556 | uint16 bpp,spp,plc,ori,reso=RESUNIT_NONE,fmt=SAMPLEFORMAT_UINT; | ^~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:653:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 653 | detail::do_tiff_read(buf,rowcount,width,is,current_row,spp); | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:656:30: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 656 | detail::do_tiff_read(buf,rowcount,width,is,current_row,spp); | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:662:12: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 662 | uint16 photometric; | ^~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:665:17: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 665 | uint16* lookuptable_red; | ^~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:666:17: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 666 | uint16* lookuptable_green; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:667:17: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 667 | uint16* lookuptable_blue; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:706:32: warning: 'int8' is deprecated [-Wdeprecated-declarations] 706 | detail::do_tiff_read(buf,rowcount,width,isr,current_row,spp); | ^~~~ /usr/include/x86_64-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:708:32: warning: 'uint8' is deprecated [-Wdeprecated-declarations] 708 | detail::do_tiff_read(buf,rowcount,width,isr,current_row,spp); | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:80:37: note: declared here 80 | typedef TIFF_MSC_DEPRECATED uint8_t uint8 TIFF_GCC_DEPRECATED; | ^~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:717:32: warning: 'int16' is deprecated [-Wdeprecated-declarations] 717 | detail::do_tiff_read(buf,rowcount,width,isr,current_row,spp); | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:719:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 719 | detail::do_tiff_read(buf,rowcount,width,isr,current_row,spp); | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:730:32: warning: 'int32' is deprecated [-Wdeprecated-declarations] 730 | detail::do_tiff_read(buf,rowcount,width,isr,current_row,spp); | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:732:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 732 | detail::do_tiff_read(buf,rowcount,width,isr,current_row,spp); | ^~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:771:12: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 771 | uint16 photometric; | ^~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:774:17: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 774 | uint16* lookuptable_red; | ^~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:775:17: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 775 | uint16* lookuptable_green; | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:776:17: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 776 | uint16* lookuptable_blue; | ^~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.cc:76: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.cc:58: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/bindings/wrap_tmalign.hh:24, from /build/openstructure-2.3.1/modules/bindings/pymod/export_tmalign.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/shared_array.hpp:19, from /usr/include/boost/shared_array.hpp:17, from /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/iomanip:40, from /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/alg_transform.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/transform.hh:24, from /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/image_format.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/image_format.cc.o -MF CMakeFiles/ost_io.dir/img/image_format.cc.o.d -o CMakeFiles/ost_io.dir/img/image_format.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/image_format.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.cc:34: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:29: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:38: /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:51:40: warning: 'int32' is deprecated [-Wdeprecated-declarations] 51 | class complexint32:public std::complex{ | ^~~~~ In file included from /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:24: /usr/include/x86_64-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:61:40: warning: 'int16' is deprecated [-Wdeprecated-declarations] 61 | class complexint16:public std::complex{ | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:71:39: warning: 'int8' is deprecated [-Wdeprecated-declarations] 71 | class complexint8:public std::complex{ | ^~~~ /usr/include/x86_64-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:105:114: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 105 | void do_tiff_read(tdata_t buf,unsigned int rps, unsigned int width, IST* is,unsigned int& current_row, uint16 spp) | ^ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc: In member function 'virtual void ost::io::MapIOJpkHandler::Import(ost::img::ImageHandle&, const boost::filesystem::path&, const ost::io::ImageFormatBase&)': /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:128:11: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 128 | uint16* reflect; | ^~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:129:11: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 129 | uint32* dummy; | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc: In member function 'virtual void ost::io::MapIOJpkHandler::Import(ost::img::MapHandle&, std::istream&, const ost::io::ImageFormatBase&)': /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:223:11: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 223 | uint16* reflect; | ^~~~~~~ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:224:11: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 224 | uint32* dummy; | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/tiff_util.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/tiff_util.cc.o -MF CMakeFiles/ost_io.dir/img/tiff_util.cc.o.d -o CMakeFiles/ost_io.dir/img/tiff_util.cc.o -c /build/openstructure-2.3.1/modules/io/src/img/tiff_util.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.cc:34: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 48%] Building CXX object modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_bindings_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o -MF CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o.d -o CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o -c /build/openstructure-2.3.1/modules/bindings/pymod/wrap_bindings.cc make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod/CMakeFiles/_ost_db.dir/DependInfo.cmake --color= make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 48%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/export_linear_db.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_db_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/pymod/CMakeFiles/_ost_db.dir/export_linear_db.cc.o -MF CMakeFiles/_ost_db.dir/export_linear_db.cc.o.d -o CMakeFiles/_ost_db.dir/export_linear_db.cc.o -c /build/openstructure-2.3.1/modules/db/pymod/export_linear_db.cc [ 48%] Building CXX object modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -MF CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o.d -o CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/pymod/wrap_seq_alg.cc [ 48%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_db_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o -MF CMakeFiles/_ost_db.dir/wrap_db.cc.o.d -o CMakeFiles/_ost_db.dir/wrap_db.cc.o -c /build/openstructure-2.3.1/modules/db/pymod/wrap_db.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.cc:34: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/iomanip:40, from /build/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:27, from /build/openstructure-2.3.1/modules/io/src/img/tiff_util.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/complex:44, from /build/openstructure-2.3.1/modules/io/src/img/tiff_util.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:51:40: warning: 'int32' is deprecated [-Wdeprecated-declarations] 51 | class complexint32:public std::complex{ | ^~~~~ In file included from /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:24: /usr/include/x86_64-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:61:40: warning: 'int16' is deprecated [-Wdeprecated-declarations] 61 | class complexint16:public std::complex{ | ^~~~~ /usr/include/x86_64-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:71:39: warning: 'int8' is deprecated [-Wdeprecated-declarations] 71 | class complexint8:public std::complex{ | ^~~~ /usr/include/x86_64-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:105:114: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 105 | void do_tiff_read(tdata_t buf,unsigned int rps, unsigned int width, IST* is,unsigned int& current_row, uint16 spp) | ^ /usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/bindings/pymod/wrap_bindings.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/db/pymod/export_linear_db.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 48%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/bindings/_ost_bindings.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_bindings.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/bindings/_ost_bindings.so CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_bindings.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/lga.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./lga.pyc\",\"lga.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/hbplus.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hbplus.pyc\",\"hbplus.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/msms.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./msms.pyc\",\"msms.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/tmtools.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./tmtools.pyc\",\"tmtools.py\",doraise=True)" In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/seq/alg/pymod/wrap_seq_alg.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/dssp.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dssp.pyc\",\"dssp.py\",doraise=True)" /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/clustalw.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./clustalw.pyc\",\"clustalw.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/utils.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./utils.pyc\",\"utils.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/naccess.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./naccess.pyc\",\"naccess.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/hhblits.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits.pyc\",\"hhblits.py\",doraise=True)" In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/db/pymod/wrap_db.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/hhblits2.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits2.pyc\",\"hhblits2.py\",doraise=True)" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:24, from /build/openstructure-2.3.1/modules/db/pymod/export_linear_db.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/hhblits3.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits3.pyc\",\"hhblits3.py\",doraise=True)" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/blast.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./blast.pyc\",\"blast.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/cadscore.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./cadscore.pyc\",\"cadscore.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/kclust.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./kclust.pyc\",\"kclust.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/ialign.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./ialign.pyc\",\"ialign.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/mmseqs2.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./mmseqs2.pyc\",\"mmseqs2.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 48%] Built target _ost_bindings In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/merge_pairwise_alignments.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/pymod/wrap_seq_alg.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/ins_del.hh:25, from /build/openstructure-2.3.1/modules/seq/alg/pymod/wrap_seq_alg.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/heuristic_block_modifiers.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 56%] Generating scene_win/moc_gfx_scene_node.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_gfx_scene_node.cpp_parameters [ 56%] Generating scene_win/moc_label_node.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_label_node.cpp_parameters [ 56%] Generating scene_win/moc_render_mode_node.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp_parameters In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/tests/test_mae_standalone.cc:2: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/io/tests/test_mae_standalone.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 56%] Generating scene_win/moc_render_modes_node.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp_parameters In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /build/openstructure-2.3.1/modules/mol/mm/src/buildingblock.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/src/forcefield.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/gromacs_block_modifiers.hh:28, from /build/openstructure-2.3.1/modules/mol/mm/src/gromacs_block_modifiers.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/gromacs_block_modifiers.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/modules/mol/mm/src/interaction.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 56%] Generating scene_win/moc_root_node.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp_parameters [ 56%] Generating scene_win/moc_scene_node.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp_parameters [ 56%] Generating scene_win/moc_scene_win.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp_parameters [ 56%] Generating scene_win/moc_scene_win_model.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp_parameters In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:26, from /build/openstructure-2.3.1/modules/mol/mm/src/simulation.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:32, from /build/openstructure-2.3.1/modules/mol/mm/src/ff_reader.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:30, from /build/openstructure-2.3.1/modules/conop/src/chemdict_tool.cc:32: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/conop/src/chemdict_tool.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 56%] Generating sequence_viewer/moc_align_properties_painter.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp_parameters [ 56%] Generating sequence_viewer/moc_alignment_view_object.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp_parameters [ 56%] Generating sequence_viewer/moc_background_painter.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp_parameters In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/tools/molck/main.cc:8: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from /build/openstructure-2.3.1/tools/molck/main.cc:2: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/iomanip:40, from /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 56%] Generating sequence_viewer/moc_base_row.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp_parameters [ 57%] Generating sequence_viewer/moc_base_view_object.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp_parameters [ 57%] Linking CXX executable ../../../stage/bin/test_mae_standalone cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mae_standalone.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o -o ../../../stage/bin/test_mae_standalone -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/tools/molck/main.cc:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24, from /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 57%] Built target test_mae_standalone [ 57%] Generating sequence_viewer/moc_conservation_painter.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp_parameters [ 57%] Generating sequence_viewer/moc_painter.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp_parameters [ 57%] Generating sequence_viewer/moc_secstr_row.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp_parameters In file included from /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:39: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 61%] Built target chemdict_tool [ 61%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -MF CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o.d -o CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/file_browser.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/observer.hh:26, from /build/openstructure-2.3.1/modules/mol/mm/src/observer.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/observer.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:28, from /build/openstructure-2.3.1/modules/mol/mm/src/system_creator.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/observer.hh:33: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 61%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology.cc.o -MF CMakeFiles/ost_mol_mm.dir/topology.cc.o.d -o CMakeFiles/ost_mol_mm.dir/topology.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/topology.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/conop/pymod/wrap_conop.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 61%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/steep.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/steep.cc.o -MF CMakeFiles/ost_mol_mm.dir/steep.cc.o.d -o CMakeFiles/ost_mol_mm.dir/steep.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/steep.cc [ 61%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_compound.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_compound.cc.o -MF CMakeFiles/_ost_conop.dir/export_compound.cc.o.d -o CMakeFiles/_ost_conop.dir/export_compound.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_compound.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:29, from /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 61%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp [ 61%] Linking CXX executable ../../../../stage/bin/lddt cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/lddt.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/lddt.dir/lddt.cc.o -o ../../../../stage/bin/lddt -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so [ 61%] Linking CXX executable ../../stage/bin/molck cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tools/molck && /usr/bin/cmake -E cmake_link_script CMakeFiles/molck.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/molck.dir/main.cc.o -o ../../stage/bin/molck -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../stage/lib/libost_io.so.2.3.1 ../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../stage/lib/libost_seq_alg.so.2.3.1 ../../stage/lib/libost_conop.so.2.3.1 ../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../stage/lib/libost_seq.so.2.3.1 ../../stage/lib/libost_mol.so.2.3.1 ../../stage/lib/libost_img_alg.so.2.3.1 ../../stage/lib/libost_img.so.2.3.1 ../../stage/lib/libost_info.so.2.3.1 ../../stage/lib/libost_base.so.2.3.1 ../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 61%] Built target lddt [ 62%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_processor.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_processor.cc.o -MF CMakeFiles/_ost_conop.dir/export_processor.cc.o.d -o CMakeFiles/_ost_conop.dir/export_processor.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_processor.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/src/topology.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 62%] Built target molck [ 62%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_heuristic.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -MF CMakeFiles/_ost_conop.dir/export_heuristic.cc.o.d -o CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_heuristic.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 62%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -MF CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o.d -o CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_amino_acids.cc [ 62%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_viewer.cpp [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gl_canvas.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/file_type_dialog.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gl_win.cpp [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o -MF CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_menu.cpp [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gosty_app.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/conop/pymod/export_compound.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/gl_canvas.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gl_canvas.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/conop/pymod/export_heuristic.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/conop/pymod/export_processor.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, from /build/openstructure-2.3.1/modules/conop/pymod/export_compound.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_area.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main_area.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main_area.cpp [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_perspective.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -MF CMakeFiles/ost_gui.dir/moc_perspective.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_perspective.cpp [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -MF CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_dock_widget.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/heuristic.hh:22, from /build/openstructure-2.3.1/modules/conop/pymod/export_heuristic.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/processor.hh:22, from /build/openstructure-2.3.1/modules/conop/pymod/export_processor.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_window.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main_window.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main_window.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/conop/pymod/export_amino_acids.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:26, from /build/openstructure-2.3.1/modules/conop/pymod/export_amino_acids.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdockwidget.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDockWidget:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/dock_widget.hh:31: /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /usr/include/c++/12/string:53, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:28: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:136:29: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/string:40: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:136:29: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:136:29: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:136:29: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:137:29: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:137:29: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:137:29: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:137:29: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 64%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_conop.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_conop.cc.o -MF CMakeFiles/_ost_conop.dir/export_conop.cc.o.d -o CMakeFiles/_ost_conop.dir/export_conop.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_conop.cc [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -MF CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main_window.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QMainWindow:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main_window.hh:35: /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_widget.cpp [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_geom_handler.cpp [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_pool.cpp [ 65%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_diag.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_diag.cc.o -MF CMakeFiles/_ost_conop.dir/export_diag.cc.o.d -o CMakeFiles/_ost_conop.dir/export_diag.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_diag.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/gosty_app.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gosty_app.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_message_widget.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 65%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/seq/alg/_ost_seq_alg.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_seq_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/seq/alg/_ost_seq_alg.so CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/mat.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./mat.pyc\",\"mat.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/renumber.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./renumber.pyc\",\"renumber.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./aaindex.pyc\",\"aaindex.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 65%] Built target _ost_seq_alg [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_message_box_widget.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/scene_selection.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_log_reader.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh: In instantiation of 'ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]': /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:40:25: required from here /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh:323:8: warning: the address of 'ost::gui::WidgetStateSaver::' will never be NULL [-Waddress] 323 | if(dynamic_cast(this)){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::' declared here 263 | class WidgetStateSaver: public BASE | ^~~~~~~~~~~~~~~~~~~~~~ [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp [ 65%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_rule_based.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_rule_based.cc.o -MF CMakeFiles/_ost_conop.dir/export_rule_based.cc.o.d -o CMakeFiles/_ost_conop.dir/export_rule_based.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_rule_based.cc [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp [ 65%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -MF CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o.d -o CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_ring_finder.cc [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/conop/pymod/export_conop.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 65%] Linking CXX shared library ../../../../stage/lib/libost_mol_mm.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/AMBER03.dat /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/forcefields/AMBER03.dat /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/CHARMM27.dat /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/forcefields/CHARMM27.dat cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_mm.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol_mm.so.2.3 -o ../../../../stage/lib/libost_mol_mm.so.2.3.1 CMakeFiles/ost_mol_mm.dir/forcefield.cc.o CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o CMakeFiles/ost_mol_mm.dir/interaction.cc.o CMakeFiles/ost_mol_mm.dir/simulation.cc.o CMakeFiles/ost_mol_mm.dir/modeller.cc.o CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o CMakeFiles/ost_mol_mm.dir/observer.cc.o CMakeFiles/ost_mol_mm.dir/system_creator.cc.o CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o CMakeFiles/ost_mol_mm.dir/topology.cc.o CMakeFiles/ost_mol_mm.dir/steep.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libboost_program_options.so ../../../../stage/lib/libost_io.so.2.3.1 /usr/lib/x86_64-linux-gnu/libOpenMM.so ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol_mm.so.2.3.1 ../../../../stage/lib/libost_mol_mm.so.2.3 ../../../../stage/lib/libost_mol_mm.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/conop/pymod/export_conop.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 65%] Built target ost_mol_mm [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/conop/pymod/export_diag.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/align_properties_painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/conservation_painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/background_painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/diag.hh:23, from /build/openstructure-2.3.1/modules/conop/pymod/export_diag.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/secstr_row.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_secstr_painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/conop/pymod/export_rule_based.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_selection_painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_text_painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/rule_based.hh:22, from /build/openstructure-2.3.1/modules/conop/pymod/export_rule_based.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/conop/pymod/export_ring_finder.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/ring_finder.hh:27, from /build/openstructure-2.3.1/modules/conop/pymod/export_ring_finder.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_row.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_main_thread_runner.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/tick_painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_search_bar.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/title_row.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_table_view.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_viewer.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_gutter.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_view_object.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/conop/_ost_conop.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_conop.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/conop/_ost_conop.so CMakeFiles/_ost_conop.dir/wrap_conop.cc.o CMakeFiles/_ost_conop.dir/export_compound.cc.o CMakeFiles/_ost_conop.dir/export_processor.cc.o CMakeFiles/_ost_conop.dir/export_heuristic.cc.o CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o CMakeFiles/_ost_conop.dir/export_conop.cc.o CMakeFiles/_ost_conop.dir/export_diag.cc.o CMakeFiles/_ost_conop.dir/export_rule_based.cc.o CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_conop.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/conop/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./__init__.pyc\",\"__init__.py\",doraise=True)" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/alignment_view_object.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/conop/pymod/cleanup.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./cleanup.pyc\",\"cleanup.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Built target _ost_conop make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/depend [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_output_redirector.cpp make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o -MF CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o.d -o CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/wrap_gfx.cc [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_path_completer.cpp [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_completer.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter_worker.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_namespace_tree_model.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:32: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_state_machine.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_state.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_transition.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_transition_guard.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_bar.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_bar.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_manager.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_bottom_bar.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_box.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_event_button.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_widget_container.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/wrap_gfx.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter_worker.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/../../../../../modules/gui/src/panels/drop_box.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_bar_widget_holder.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/gfx/pymod/wrap_gfx.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_shell_widget.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_side_bar.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/transition.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_transition.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_splitter_panel_bar.cpp /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_tabbed_panel_bar.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/transition_guard.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_transition_guard.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_gfx_scene_node.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_label_node.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/context_menu.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp [ 71%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene.cc.o In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/custom_part_node.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene.cc.o -MF CMakeFiles/_ost_gfx.dir/export_scene.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_scene.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_scene.cc /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/current_selection_node.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp [ 73%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_node.cc [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_option_group.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_part_node.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_node.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_bar.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_modes_node.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_option.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/scene_win.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/scene_win_model.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_widget.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_argand.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_argand.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_argand.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_argand.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool_bar.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_bar.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_manager_gui.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool_manager.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_node.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_scene.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_null_overlay.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_base.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/argand.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/info_panel.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gfx/pymod/export_scene.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/thin_splitter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/thin_splitter.cc.o -MF CMakeFiles/ost_gui.dir/thin_splitter.cc.o.d -o CMakeFiles/ost_gui.dir/thin_splitter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/thin_splitter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/measure_tool.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool_options_win.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/perspective.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/perspective.cc.o -MF CMakeFiles/ost_gui.dir/perspective.cc.o.d -o CMakeFiles/ost_gui.dir/perspective.cc.o -c /build/openstructure-2.3.1/modules/gui/src/perspective.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data_observer.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/fft_panel.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/measure_tool.hh:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_registry.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_registry.cc.o -MF CMakeFiles/ost_gui.dir/widget_registry.cc.o.d -o CMakeFiles/ost_gui.dir/widget_registry.cc.o -c /build/openstructure-2.3.1/modules/gui/src/widget_registry.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/pointlist_overlay_base.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp:10: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_browser.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_browser.cc.o -MF CMakeFiles/ost_gui.dir/file_browser.cc.o.d -o CMakeFiles/ost_gui.dir/file_browser.cc.o -c /build/openstructure-2.3.1/modules/gui/src/file_browser.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -MF CMakeFiles/ost_gui.dir/file_type_dialog.cc.o.d -o CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -c /build/openstructure-2.3.1/modules/gui/src/file_type_dialog.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_viewer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_viewer.cc.o -MF CMakeFiles/ost_gui.dir/file_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/file_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/file_viewer.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main.cc.o -MF CMakeFiles/ost_gui.dir/main.cc.o.d -o CMakeFiles/ost_gui.dir/main.cc.o -c /build/openstructure-2.3.1/modules/gui/src/main.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer.hh:37: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QMainWindow:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:35: /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_canvas.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gl_canvas.cc.o -MF CMakeFiles/ost_gui.dir/gl_canvas.cc.o.d -o CMakeFiles/ost_gui.dir/gl_canvas.cc.o -c /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/dock_widget.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/dock_widget.cc.o -MF CMakeFiles/ost_gui.dir/dock_widget.cc.o.d -o CMakeFiles/ost_gui.dir/dock_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/dock_widget.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main_window.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main_window.cc.o -MF CMakeFiles/ost_gui.dir/main_window.cc.o.d -o CMakeFiles/ost_gui.dir/main_window.cc.o -c /build/openstructure-2.3.1/modules/gui/src/main_window.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o -MF CMakeFiles/ost_gui.dir/gl_win.cc.o.d -o CMakeFiles/ost_gui.dir/gl_win.cc.o -c /build/openstructure-2.3.1/modules/gui/src/gl_win.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o -MF CMakeFiles/ost_gui.dir/scene_menu.cc.o.d -o CMakeFiles/ost_gui.dir/scene_menu.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_menu.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/modules/gui/src/file_type_dialog.hh:31, from /build/openstructure-2.3.1/modules/gui/src/file_type_dialog.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/openstructure-2.3.1/modules/gui/src/file_type_dialog.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_browser.hh:23, from /build/openstructure-2.3.1/modules/gui/src/perspective.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/platform.hh:22, from /build/openstructure-2.3.1/modules/gui/src/perspective.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget.cc.o -MF CMakeFiles/ost_gui.dir/widget.cc.o.d -o CMakeFiles/ost_gui.dir/widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/widget.cc [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/admin.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/admin.cc.o -MF CMakeFiles/ost_gui.dir/admin.cc.o.d -o CMakeFiles/ost_gui.dir/admin.cc.o -c /build/openstructure-2.3.1/modules/gui/src/admin.cc [ 76%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -MF CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_symmetry_node.cc In file included from /build/openstructure-2.3.1/modules/gui/src/dock_widget.cc:25: /build/openstructure-2.3.1/modules/gui/src/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdockwidget.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDockWidget:1, from /build/openstructure-2.3.1/modules/gui/src/dock_widget.hh:31: /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /build/openstructure-2.3.1/modules/gui/src/main_window.cc:25: /build/openstructure-2.3.1/modules/gui/src/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QMainWindow:1, from /build/openstructure-2.3.1/modules/gui/src/main_window.hh:35: /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /build/openstructure-2.3.1/modules/gui/src/main_window.cc:26: /build/openstructure-2.3.1/modules/gui/src/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); | ^ /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ /build/openstructure-2.3.1/modules/gui/src/dock_widget.hh: In member function 'void ost::gui::MainWindow::AddDockWidget(QWidget*, const QString&, bool, int)': /build/openstructure-2.3.1/modules/gui/src/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); | ^ /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ /build/openstructure-2.3.1/modules/gui/src/main_window.cc:71:33: warning: 'QVariant qVariantFromValue(const T&) [with T = QDockWidget*]' is deprecated: Use QVariant::fromValue() instead. [-Wdeprecated-declarations] 71 | act->setData(qVariantFromValue((QDockWidget*)dock)); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qaction.h:47, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qmenu.h:47, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QMenu:1, from /build/openstructure-2.3.1/modules/gui/src/main_window.hh:36: /usr/include/x86_64-linux-gnu/qt5/QtCore/qvariant.h:530:17: note: declared here 530 | inline QVariant qVariantFromValue(const T &t) | ^~~~~~~~~~~~~~~~~ [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_pool.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_pool.cc.o -MF CMakeFiles/ost_gui.dir/widget_pool.cc.o.d -o CMakeFiles/ost_gui.dir/widget_pool.cc.o -c /build/openstructure-2.3.1/modules/gui/src/widget_pool.cc [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -MF CMakeFiles/ost_gui.dir/messages/message_widget.cc.o.d -o CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/messages/message_widget.cc [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -MF CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o.d -o CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.cc [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/log_reader.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/log_reader.cc.o -MF CMakeFiles/ost_gui.dir/messages/log_reader.cc.o.d -o CMakeFiles/ost_gui.dir/messages/log_reader.cc.o -c /build/openstructure-2.3.1/modules/gui/src/messages/log_reader.cc [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/main.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.cc [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/gl_canvas.hh:23, from /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/scene_menu.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/gl_win.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:30, from /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:34: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_symmetry_node.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(QWidget*)': /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:62:13: warning: 'QDirModel::QDirModel(QObject*)' is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] 62 | model_(new QDirModel), | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDirModel:1, from /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:53: /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); | ^~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(const QString&, QWidget*)': /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:102:13: warning: 'QDirModel::QDirModel(QObject*)' is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] 102 | model_(new QDirModel), | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); | ^~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:24, from /build/openstructure-2.3.1/modules/gui/src/main.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/glwin_base.hh:28, from /build/openstructure-2.3.1/modules/gui/src/gl_canvas.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/symmetry_node.hh:22, from /build/openstructure-2.3.1/modules/gfx/pymod/export_symmetry_node.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.cc [ 78%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_obj.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/smart_ptr/weak_ptr.hpp:17, from /usr/include/boost/smart_ptr/enable_shared_from_this.hpp:16, from /usr/include/boost/enable_shared_from_this.hpp:16, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:29: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.hh:27, from /build/openstructure-2.3.1/modules/gui/src/main.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.cc:23: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/main.cc: In static member function 'static QSize ost::gui::GostyMainWindow::GetDefaultSize()': /build/openstructure-2.3.1/modules/gui/src/main.cc:59:64: warning: 'const QRect QDesktopWidget::availableGeometry(int) const' is deprecated: Use QGuiApplication::screens() [-Wdeprecated-declarations] 59 | QRect desktop_geom=QApplication::desktop()->availableGeometry(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDesktopWidget:1, from /build/openstructure-2.3.1/modules/gui/src/main.cc:35: /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdesktopwidget.h:88:67: note: declared here 88 | QT_DEPRECATED_X("Use QGuiApplication::screens()") const QRect availableGeometry(int screen = -1) const; | ^~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_op.hh:29, from /build/openstructure-2.3.1/modules/gui/src/scene_menu.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/messages/message_widget.cc:23: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh: In instantiation of 'ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]': /build/openstructure-2.3.1/modules/gui/src/main.cc:69:69: required from here /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:323:8: warning: the address of 'ost::gui::WidgetStateSaver::' will never be NULL [-Waddress] 323 | if(dynamic_cast(this)){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::' declared here 263 | class WidgetStateSaver: public BASE | ^~~~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc: In member function 'void ost::gui::GLCanvas::HandleMouseMoveEvent(QMouseEvent*)': /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:373:32: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 373 | if (event->buttons() & Qt::MidButton) { | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:399:37: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 399 | } else if (event->buttons() & Qt::MidButton) { | ^~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc: In member function 'virtual void ost::gui::GLCanvas::wheelEvent(QWheelEvent*)': /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:488:50: warning: 'int QWheelEvent::delta() const' is deprecated: Use angleDelta() [-Wdeprecated-declarations] 488 | 0.2*static_cast(-event->delta())); | ~~~~~~~~~~~~^~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtGui/QMouseEvent:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:25: /usr/include/x86_64-linux-gnu/qt5/QtGui/qevent.h:219:16: note: declared here 219 | inline int delta() const { return qt4D; } | ^~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh: In instantiation of 'void ost::gui::WidgetStateSaver::set_state_() [with BASE = QMainWindow]': /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:286:5: required from 'ost::gui::WidgetStateSaver::WidgetStateSaver(const QString&, QPoint, QSize, QWidget*) [with BASE = QMainWindow]' /build/openstructure-2.3.1/modules/gui/src/main.cc:69:69: required from here /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:305:10: warning: the address of 'ost::gui::WidgetStateSaver::' will never be NULL [-Waddress] 305 | if(dynamic_cast(this)){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::' declared here 263 | class WidgetStateSaver: public BASE | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gui/src/gl_win.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gl_canvas.hh:23, from /build/openstructure-2.3.1/modules/gui/src/gl_win.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.cc [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.cc [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.cc [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_obj.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_obj.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh:26, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 79%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_entity.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_entity.cc.o -MF CMakeFiles/_ost_gfx.dir/export_entity.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_entity.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_entity.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh:29, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh:32, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.cc [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o -c /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:23: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gosty_app.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gosty_app.cc.o -MF CMakeFiles/ost_gui.dir/gosty_app.cc.o.d -o CMakeFiles/ost_gui.dir/gosty_app.cc.o -c /build/openstructure-2.3.1/modules/gui/src/gosty_app.cc /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.cc: In member function 'virtual int ost::gui::SequenceTableView::sizeHintForColumn(int) const': /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.cc:480:35: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 480 | return this->fontMetrics().width('W'); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtGui/qpainter.h:59, from /usr/include/x86_64-linux-gnu/qt5/QtGui/QPainter:1, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:30, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:35: /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main_area.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main_area.cc.o -MF CMakeFiles/ost_gui.dir/main_area.cc.o.d -o CMakeFiles/ost_gui.dir/main_area.cc.o -c /build/openstructure-2.3.1/modules/gui/src/main_area.cc [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_state_saver.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_state_saver.cc.o -MF CMakeFiles/ost_gui.dir/widget_state_saver.cc.o.d -o CMakeFiles/ost_gui.dir/widget_state_saver.cc.o -c /build/openstructure-2.3.1/modules/gui/src/widget_state_saver.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:142, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QtCore:4, from /usr/include/x86_64-linux-gnu/qt5/QtGui/QtGuiDepends:3, from /usr/include/x86_64-linux-gnu/qt5/QtGui/QtGui:3, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:26, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:39: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o -MF CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o.d -o CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o -c /build/openstructure-2.3.1/modules/gui/src/widget_geom_handler.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc: In member function 'void ost::gui::SequenceViewer::MouseWheelEvent(QWheelEvent*)': /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:298:27: warning: 'int QWheelEvent::delta() const' is deprecated: Use angleDelta() [-Wdeprecated-declarations] 298 | int delta = event->delta(); | ~~~~~~~~~~~~^~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtGui/QWheelEvent:1, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh:32, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:42: /usr/include/x86_64-linux-gnu/qt5/QtGui/qevent.h:219:16: note: declared here 219 | inline int delta() const { return qt4D; } | ^~~~~ /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:299:25: warning: 'Qt::Orientation QWheelEvent::orientation() const' is deprecated: Use angleDelta() [-Wdeprecated-declarations] 299 | if (event->orientation() == Qt::Vertical) { | ~~~~~~~~~~~~~~~~~~^~ /usr/include/x86_64-linux-gnu/qt5/QtGui/qevent.h:222:28: note: declared here 222 | inline Qt::Orientation orientation() const { return qt4O; } | ^~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/pymod/export_entity.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_loader.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_loader.cc.o -MF CMakeFiles/ost_gui.dir/file_loader.cc.o.d -o CMakeFiles/ost_gui.dir/file_loader.cc.o -c /build/openstructure-2.3.1/modules/gui/src/file_loader.cc [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_bar.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/button_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/button_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/button_bar.cc [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/drop_box.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/drop_box.cc.o -MF CMakeFiles/ost_gui.dir/panels/drop_box.cc.o.d -o CMakeFiles/ost_gui.dir/panels/drop_box.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh:32, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.cc:32: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 82%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_surface.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_surface.cc.o -MF CMakeFiles/_ost_gfx.dir/export_surface.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_surface.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_surface.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/modules/gui/src/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/gosty_app.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/bottom_bar.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_box.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_box.cc.o -MF CMakeFiles/ost_gui.dir/panels/button_box.cc.o.d -o CMakeFiles/ost_gui.dir/panels/button_box.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/button_box.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/event_button.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/event_button.cc.o -MF CMakeFiles/ost_gui.dir/panels/event_button.cc.o.d -o CMakeFiles/ost_gui.dir/panels/event_button.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/event_button.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh:22, from /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /usr/include/boost/ptr_container/ptr_vector.hpp:19, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/panel_manager.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/panel_widget_container.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/scene_selection.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh:27, from /build/openstructure-2.3.1/modules/gui/src/gosty_app.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh:23, from /build/openstructure-2.3.1/modules/gui/src/gosty_app.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /build/openstructure-2.3.1/modules/gui/src/gosty_app.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/side_bar.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/side_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/side_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/side_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/side_bar.cc /build/openstructure-2.3.1/modules/gui/src/panels/event_button.cc: In member function 'virtual void ost::gui::EventButton::mouseMoveEvent(QMouseEvent*)': /build/openstructure-2.3.1/modules/gui/src/panels/event_button.cc:50:15: warning: 'Qt::DropAction QDrag::start(Qt::DropActions)' is deprecated: Use QDrag::exec() instead [-Wdeprecated-declarations] 50 | drag->start(Qt::MoveAction); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtGui/QDrag:1, from /build/openstructure-2.3.1/modules/gui/src/panels/event_button.cc:22: /usr/include/x86_64-linux-gnu/qt5/QtGui/qdrag.h:79:20: note: declared here 79 | Qt::DropAction start(Qt::DropActions supportedActions = Qt::CopyAction); | ^~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/file_loader.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/splitter_panel_bar.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/splitter_panel_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/splitter_panel_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/splitter_panel_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/splitter_panel_bar.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/openstructure-2.3.1/modules/gui/src/gosty_app.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:49: /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_op.hh:29, from /build/openstructure-2.3.1/modules/gui/src/scene_selection.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_option_group.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_surface.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_options.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_options.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_options.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/openstructure-2.3.1/modules/gui/src/scene_selection.cc:34: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:49, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_option.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_option.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_option.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gui/src/file_loader.hh:24, from /build/openstructure-2.3.1/modules/gui/src/file_loader.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/surface.hh:31, from /build/openstructure-2.3.1/modules/gfx/pymod/export_surface.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh:22, from /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/modules/gui/src/file_loader.hh:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o -MF CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o.d -o CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/openstructure-2.3.1/modules/gui/src/file_loader.cc:51: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:49, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/manipulator.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/manipulator.cc.o -MF CMakeFiles/ost_gui.dir/tools/manipulator.cc.o.d -o CMakeFiles/ost_gui.dir/tools/manipulator.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_widget.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.hh:24, from /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/modules/gui/src/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/tool.cc:19: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.cc:19: /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/gutter.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/completer_base.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.hh:26, from /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.cc /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc: In member function 'void ost::gui::OutputRedirector::Write(const String&)': /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:42:22: warning: 'int QTime::elapsed() const' is deprecated: Use QElapsedTimer instead [-Wdeprecated-declarations] 42 | if(timer_.elapsed()>1000){ | ~~~~~~~~~~~~~~^~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:25: /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:237:54: note: declared here 237 | QT_DEPRECATED_X("Use QElapsedTimer instead") int elapsed() const; | ^~~~~~~ /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:46:21: warning: 'int QTime::restart()' is deprecated: Use QElapsedTimer instead [-Wdeprecated-declarations] 46 | timer_.restart(); | ~~~~~~~~~~~~~~^~ /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:236:54: note: declared here 236 | QT_DEPRECATED_X("Use QElapsedTimer instead") int restart(); | ^~~~~~~ /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:52:17: warning: 'void QTime::start()' is deprecated: Use QElapsedTimer instead [-Wdeprecated-declarations] 52 | timer_.start(); | ~~~~~~~~~~~~^~ /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:235:55: note: declared here 235 | QT_DEPRECATED_X("Use QElapsedTimer instead") void start(); | ^~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/path_completer.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_context_parser.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 84%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primitives.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -MF CMakeFiles/_ost_gfx.dir/export_primitives.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_primitives.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh:26, from /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.cc: In constructor 'ost::gui::OstDirModel::OstDirModel(QObject*)': /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.cc:31:18: warning: 'QDirModel::QDirModel(QObject*)' is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] 31 | QDirModel(parent) | ^ In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDirModel:1, from /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.hh:26, from /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.cc:23: /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); | ^~~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_completer.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_model.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_item.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh:27, from /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, from /build/openstructure-2.3.1/modules/gui/src/python_shell/gutter.cc:22: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_text_document_layout.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh:24, from /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.hh:29, from /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_tokenizer.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/python_syntax_highlighter.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_primitives.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/primitives.hh:22, from /build/openstructure-2.3.1/modules/gfx/pymod/export_primitives.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 85%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primlist.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -MF CMakeFiles/_ost_gfx.dir/export_primlist.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_primlist.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/shell_history.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/string_literal_positions.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_model.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/state_machine.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/state.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/state.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/state.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_item.hh:25, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_item.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/transition.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/transition.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/transition.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o -c /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.cc:24: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_model.cc: In member function 'virtual Qt::ItemFlags ost::gui::PythonNamespaceTreeModel::flags(const QModelIndex&) const': /build/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_model.cc:110:12: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::ItemFlag; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 110 | return 0; | ^ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:49, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:33: /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ [ 87%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -MF CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_scene_observer.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_node.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/label_node.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.cc /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc: In constructor 'ost::gui::PythonShellWidget::PythonShellWidget(QWidget*)': /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc:79:34: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 79 | setTabStopWidth(2*metrics.width(" ")); | ~~~~~~~~~~~~~^~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qwidget.h:50, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qframe.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qabstractscrollarea.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtextedit.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qplaintextedit.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QPlainTextEdit:1, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:34: /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc:79:18: warning: 'void QPlainTextEdit::setTabStopWidth(int)' is deprecated [-Wdeprecated-declarations] 79 | setTabStopWidth(2*metrics.width(" ")); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qplaintextedit.h:179:24: note: declared here 179 | QT_DEPRECATED void setTabStopWidth(int width); | ^~~~~~~~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc: In member function 'void ost::gui::PythonShellWidget::SetTabWidth(int)': /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc:537:43: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 537 | setTabStopWidth(tab_width_*metrics.width(" ")); | ~~~~~~~~~~~~~^~~~~ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc:537:18: warning: 'void QPlainTextEdit::setTabStopWidth(int)' is deprecated [-Wdeprecated-declarations] 537 | setTabStopWidth(tab_width_*metrics.width(" ")); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qplaintextedit.h:179:24: note: declared here 179 | QT_DEPRECATED void setTabStopWidth(int width); | ^~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_primlist.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/transition.hh:23, from /build/openstructure-2.3.1/modules/gui/src/python_shell/state.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/prim_list.hh:28, from /build/openstructure-2.3.1/modules/gfx/pymod/export_primlist.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.hh:23, from /build/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/pointer_cast.hpp:52, from /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, from /build/openstructure-2.3.1/modules/gui/src/python_shell/transition.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.hh:24, from /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gui/src/scene_win/label_node.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/openstructure-2.3.1/modules/gui/src/scene_win/label_node.hh:23, from /build/openstructure-2.3.1/modules/gui/src/scene_win/label_node.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_scene_observer.cc:1: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.hh:23, from /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:28, from /build/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node_fw.hh:25, from /build/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.hh:23, from /build/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o -c /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.cc [ 88%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_render_options.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -MF CMakeFiles/_ost_gfx.dir/export_render_options.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_render_options.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/map_tool.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/map_tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/map_tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/map_tool.cc.o -c /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 88%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color.cc.o -MF CMakeFiles/_ost_gfx.dir/export_color.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_color.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_color.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/argand.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.hh:23, from /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/argand.hh:30, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/argand.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/argand.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh:28, from /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc:23: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_render_options.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.hh:28, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_color.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.cc: In member function 'virtual QMimeData* ost::gui::SceneWinModel::mimeData(const QModelIndexList&) const': /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.cc:231:26: warning: 'QByteArray& QByteArray::append(const QString&)' is deprecated: Use QString's toUtf8(), toLatin1() or toLocal8Bit() [-Wdeprecated-declarations] 231 | encoded_data.append(text); | ~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qobject.h:47, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QObject:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh:24, from /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh:34: /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:1511:20: note: declared here 1511 | inline QByteArray &QByteArray::append(const QString &s) | ^~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:26: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_slab.hh:29, from /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/platform.hh:22, from /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/pymod/export_color.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_selection.hh:23, from /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /usr/include/boost/format.hpp:17, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc: In member function 'void ost::gui::SceneWin::RowsInserted(const QModelIndex&, int, int)': /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc:117:31: warning: 'QModelIndex QModelIndex::child(int, int) const' is deprecated: Use QAbstractItemModel::index [-Wdeprecated-declarations] 117 | model->select(parent.child(start,0),QItemSelectionModel::ClearAndSelect|QItemSelectionModel::Rows); | ~~~~~~~~~~~~^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/QModelIndex:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:34, from /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc:26: /usr/include/x86_64-linux-gnu/qt5/QtCore/qabstractitemmodel.h:455:20: note: declared here 455 | inline QModelIndex QModelIndex::child(int arow, int acolumn) const | ^~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/null_overlay.cc /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc: In member function 'virtual void ost::img::gui::DataViewerPanelBase::paintEvent(QPaintEvent*)': /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:440:56: warning: 'static bool QPixmapCache::find(const QString&, QPixmap&)' is deprecated: Use bool find(const QString &, QPixmap *) instead [-Wdeprecated-declarations] 440 | if (update_raster_image_ || ( !QPixmapCache::find(cache_key, pm))) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtGui/QPixmapCache:1, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:40: /usr/include/x86_64-linux-gnu/qt5/QtGui/qpixmapcache.h:81:17: note: declared here 81 | static bool find(const QString &key, QPixmap &pixmap); | ^~~~ /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc: In member function 'virtual void ost::img::gui::DataViewerPanelBase::mouseMoveEvent(QMouseEvent*)': /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:602:38: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 602 | } else if((event->buttons() == Qt::MidButton) && HasSelection()) { | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qobjectdefs.h:48, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qwindowdefs.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qwidget.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QWidget:1, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:46, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:34: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc: In member function 'virtual void ost::img::gui::DataViewerPanelBase::wheelEvent(QWheelEvent*)': /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:613:18: warning: 'int QWheelEvent::delta() const' is deprecated: Use angleDelta() [-Wdeprecated-declarations] 613 | if(event->delta()>0) { | ~~~~~~~~~~~~^~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtGui/QResizeEvent:1, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:36: /usr/include/x86_64-linux-gnu/qt5/QtGui/qevent.h:219:16: note: declared here 219 | inline int delta() const { return qt4D; } | ^~~~~ /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc: In member function 'void ost::img::gui::DataViewerPanelBase::draw_pixel_values(QPainter&)': /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:1074:49: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 1074 | int string_w=painter.fontMetrics().width(value_string); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qwidget.h:50: /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:1090:49: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 1090 | int string_w=painter.fontMetrics().width(value_string); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_slab.hh:26: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:36: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.cc In file included from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:37: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:49, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.hh:37, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:41: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc: In constructor 'ost::img::gui::DataViewer::DataViewer(QWidget*, const ost::img::ImageHandle&, const QString&)': /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:75:14: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 75 | lastmouse_() | ^ /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc: In member function 'void ost::img::gui::DataViewer::build(const ost::img::ImageHandle&)': /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:315:54: warning: 'const QRect QDesktopWidget::availableGeometry(int) const' is deprecated: Use QGuiApplication::screens() [-Wdeprecated-declarations] 315 | resize(QApplication::desktop()->availableGeometry().adjusted(20,20,-20,-20).size()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDesktopWidget:1, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:53: /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdesktopwidget.h:88:67: note: declared here 88 | QT_DEPRECATED_X("Use QGuiApplication::screens()") const QRect availableGeometry(int screen = -1) const; | ^~~~~~~~~~~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_gui.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/circle_mask.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/mask_visitor.hh:28, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay_base.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.hh:26, from /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:25: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o -c /build/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.cc [ 91%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gradient.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gradient.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_gradient.cc [ 91%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -MF CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_color_ops.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.hh:29, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 91%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -MF CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_glwin_base.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay_base.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 91%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -MF CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/wrap_mol_alg.cc [ 92%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_exporter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -MF CMakeFiles/_ost_gfx.dir/export_exporter.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_exporter.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 92%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -MF CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_bitmap.cc [ 92%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_map.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_map.cc.o -MF CMakeFiles/_ost_gfx.dir/export_map.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_map.cc.o -c /build/openstructure-2.3.1/modules/gfx/pymod/export_map.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 92%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_svd_superpose.cc [ 92%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_clash.cc [ 92%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_trajectory_analysis.cc [ 92%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem 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/usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_gradient.cc:24: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_glwin_base.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 92%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_accessibility.cc /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_color_ops.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. 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/usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gradient.hh:28, from /build/openstructure-2.3.1/modules/gfx/pymod/export_gradient.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, from /build/openstructure-2.3.1/modules/gfx/pymod/export_color_ops.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/alg/pymod/wrap_mol_alg.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_exporter.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_bitmap.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 93%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_non_standard.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:23, from /build/openstructure-2.3.1/modules/mol/alg/pymod/wrap_mol_alg.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gfx/pymod/export_map.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_trajectory_analysis.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_svd_superpose.cc:23: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_structure_analysis.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_iso.hh:28, from /build/openstructure-2.3.1/modules/gfx/pymod/export_map.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 93%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_clash.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/trajectory_analysis.hh:29, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_trajectory_analysis.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_svd_superpose.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_sec_structure.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/structure_analysis.hh:28, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_structure_analysis.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/clash_score.hh:26, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_clash.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_sec_structure.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 93%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_membrane.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_accessibility.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_contact_overlap.cc:1: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_accessibility.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/contact_overlap.hh:6, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_contact_overlap.cc:4: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/contact_overlap.hh:8: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 93%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/pymod/export_entity_to_density.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_non_standard.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_non_standard.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_gui.so.2.3.1 ../../../stage/lib/libost_gui.so.2.3 ../../../stage/lib/libost_gui.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] Built target ost_gui make -f modules/gui/src/CMakeFiles/gosty.dir/build.make modules/gui/src/CMakeFiles/gosty.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] Generating qrc_dngr.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/rcc --name dngr --output /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/qrc_dngr.cpp /build/openstructure-2.3.1/modules/gui/src/dngr.qrc [ 93%] Generating moc_gosty.cpp cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gosty.cpp_parameters cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/gosty.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gui/src/CMakeFiles/gosty.dir/build.make modules/gui/src/CMakeFiles/gosty.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] Building CXX object modules/gui/src/CMakeFiles/gosty.dir/gosty.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gui/src/CMakeFiles/gosty.dir/gosty.cc.o -MF CMakeFiles/gosty.dir/gosty.cc.o.d -o CMakeFiles/gosty.dir/gosty.cc.o -c /build/openstructure-2.3.1/modules/gui/src/gosty.cc [ 93%] Building CXX object modules/gui/src/CMakeFiles/gosty.dir/moc_gosty.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gui/src/CMakeFiles/gosty.dir/moc_gosty.cpp.o -MF CMakeFiles/gosty.dir/moc_gosty.cpp.o.d -o CMakeFiles/gosty.dir/moc_gosty.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/moc_gosty.cpp [ 93%] Building CXX object modules/gui/src/CMakeFiles/gosty.dir/qrc_dngr.cpp.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gui/src/CMakeFiles/gosty.dir/qrc_dngr.cpp.o -MF CMakeFiles/gosty.dir/qrc_dngr.cpp.o.d -o CMakeFiles/gosty.dir/qrc_dngr.cpp.o -c /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/qrc_dngr.cpp In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/molck.hh:23, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_membrane.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/find_membrane.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_membrane.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_entity_to_density.cc:23: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/entity_to_density.hh:4, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_entity_to_density.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/modules/gui/src/gosty.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 94%] Linking CXX executable ../../../stage/lib/openstructure/libexec/gosty cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gosty.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/gosty.dir/gosty.cc.o CMakeFiles/gosty.dir/moc_gosty.cpp.o CMakeFiles/gosty.dir/qrc_dngr.cpp.o -o ../../../stage/lib/openstructure/libexec/gosty -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_gui.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_gfx.so.2.3.1 /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 94%] Built target gosty [ 94%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/gfx/_ost_gfx.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/pymod/gradients.xml /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/scene/gradients.xml cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_gfx.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/gfx/_ost_gfx.so CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o CMakeFiles/_ost_gfx.dir/export_scene.cc.o CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o CMakeFiles/_ost_gfx.dir/export_entity.cc.o CMakeFiles/_ost_gfx.dir/export_surface.cc.o CMakeFiles/_ost_gfx.dir/export_primitives.cc.o CMakeFiles/_ost_gfx.dir/export_primlist.cc.o CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o CMakeFiles/_ost_gfx.dir/export_render_options.cc.o CMakeFiles/_ost_gfx.dir/export_color.cc.o CMakeFiles/_ost_gfx.dir/export_gradient.cc.o CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o CMakeFiles/_ost_gfx.dir/export_exporter.cc.o CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o CMakeFiles/_ost_gfx.dir/export_map.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_gfx.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gfx/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gfx/pymod/py_gfx_obj.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./py_gfx_obj.pyc\",\"py_gfx_obj.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 94%] Built target _ost_gfx [ 94%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/mol/alg/_ost_mol_alg.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/mol/alg/_ost_mol_alg.so CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libsqlite3.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/views.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./views.pyc\",\"views.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/superpose.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./superpose.pyc\",\"superpose.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/qsscoring.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./qsscoring.pyc\",\"qsscoring.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/trajectory_analysis.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./trajectory_analysis.pyc\",\"trajectory_analysis.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/structure_analysis.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./structure_analysis.pyc\",\"structure_analysis.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/helix_kinks.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./helix_kinks.pyc\",\"helix_kinks.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/hbond.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./hbond.pyc\",\"hbond.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 94%] Built target _ost_mol_alg make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod/CMakeFiles/_ost_io.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 94%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/wrap_io.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/wrap_io.cc.o -MF CMakeFiles/_ost_io.dir/wrap_io.cc.o.d -o CMakeFiles/_ost_io.dir/wrap_io.cc.o -c /build/openstructure-2.3.1/modules/io/pymod/wrap_io.cc [ 94%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_pdb_io.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_pdb_io.cc.o -MF CMakeFiles/_ost_io.dir/export_pdb_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_pdb_io.cc.o -c /build/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc [ 94%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o [ 96%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_omf_io.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o -MF CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o -c /build/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_omf_io.cc.o -MF CMakeFiles/_ost_io.dir/export_omf_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_omf_io.cc.o -c /build/openstructure-2.3.1/modules/io/pymod/export_omf_io.cc [ 96%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_map_io.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_map_io.cc.o -MF CMakeFiles/_ost_io.dir/export_map_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_map_io.cc.o -c /build/openstructure-2.3.1/modules/io/pymod/export_map_io.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/io/pymod/export_map_io.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/io/pymod/wrap_io.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/io/pymod/export_omf_io.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh:26, from /build/openstructure-2.3.1/modules/io/pymod/export_map_io.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, from /build/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25, from /build/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/pymod/wrap_io.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, from /build/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh:26, from /build/openstructure-2.3.1/modules/io/pymod/export_omf_io.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mmcif_info.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 96%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/io/_ost_io.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_io.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/io/_ost_io.so CMakeFiles/_ost_io.dir/wrap_io.cc.o CMakeFiles/_ost_io.dir/export_pdb_io.cc.o CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o CMakeFiles/_ost_io.dir/export_omf_io.cc.o CMakeFiles/_ost_io.dir/export_map_io.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/io/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/io/pymod/remote.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./remote.pyc\",\"remote.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/io/pymod/repository.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./repository.pyc\",\"repository.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target _ost_io make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/depend make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_forcefield.cc [ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/_ost_gui.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_settings.cc [ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_simulation.cc make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o [ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_openmm.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_observers.cc [ 96%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/wrap_gui.cc.o [ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_interaction.cc [ 97%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/wrap_gui.cc.o -MF CMakeFiles/_ost_gui.dir/wrap_gui.cc.o.d -o CMakeFiles/_ost_gui.dir/wrap_gui.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/wrap_gui.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_ff_reader.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o -MF CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o.d -o CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_alignment_view.cc [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_message_widget.cc.o [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_win.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_message_widget.cc.o -MF CMakeFiles/_ost_gui.dir/export_message_widget.cc.o.d -o CMakeFiles/_ost_gui.dir/export_message_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_message_widget.cc [ 97%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_win.cc.o -MF CMakeFiles/_ost_gui.dir/export_gl_win.cc.o.d -o CMakeFiles/_ost_gui.dir/export_gl_win.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_gl_win.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_buildingblock.cc [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_tool.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_tool.cc.o -MF CMakeFiles/_ost_gui.dir/export_tool.cc.o.d -o CMakeFiles/_ost_gui.dir/export_tool.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_tool.cc [ 97%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_block_modifiers.cc [ 97%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_topology.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_message_widget.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_gl_win.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_interaction.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_block_modifiers.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/wrap_gui.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_openmm.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_ff_reader.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_settings.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_tool.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_topology.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_forcefield.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_observers.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_buildingblock.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_alignment_view.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_simulation.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/block_modifiers.hh:23, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_block_modifiers.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_interaction.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:32, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_ff_reader.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_settings.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_py_shell.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_py_shell.cc.o -MF CMakeFiles/_ost_gui.dir/export_py_shell.cc.o.d -o CMakeFiles/_ost_gui.dir/export_py_shell.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_py_shell.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_topology.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_buildingblock.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /build/openstructure-2.3.1/modules/gui/pymod/export_alignment_view.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:26, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_simulation.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/pymod/export_tool.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/observer.hh:26, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_observers.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_forcefield.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gosty.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gosty.cc.o -MF CMakeFiles/_ost_gui.dir/export_gosty.cc.o.d -o CMakeFiles/_ost_gui.dir/export_gosty.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_topology.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/observer.hh:33: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_win.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_win.cc.o -MF CMakeFiles/_ost_gui.dir/export_scene_win.cc.o.d -o CMakeFiles/_ost_gui.dir/export_scene_win.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_scene_win.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o -MF CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o.d -o CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_sequence_viewer.cc [ 98%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_modeller.cc [ 98%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o -MF CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/wrap_mol_mm.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_py_shell.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_perspective.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_perspective.cc.o -MF CMakeFiles/_ost_gui.dir/export_perspective.cc.o.d -o CMakeFiles/_ost_gui.dir/export_perspective.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_perspective.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o -MF CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o.d -o CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_sip_handler.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o -MF CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o.d -o CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_scene_selection.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_scene_win.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_main_area.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_main_area.cc.o -MF CMakeFiles/_ost_gui.dir/export_main_area.cc.o.d -o CMakeFiles/_ost_gui.dir/export_main_area.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_main_area.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh:23, from /build/openstructure-2.3.1/modules/gui/pymod/export_scene_win.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_sequence_viewer.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh:23, from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_panels.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_panels.cc.o -MF CMakeFiles/_ost_gui.dir/export_panels.cc.o.d -o CMakeFiles/_ost_gui.dir/export_panels.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_panels.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh:27, from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /build/openstructure-2.3.1/modules/gui/pymod/export_sequence_viewer.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:32: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_modeller.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/mol/mm/pymod/wrap_mol_mm.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o -MF CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o.d -o CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_menu_bar.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_loader.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_loader.cc.o -MF CMakeFiles/_ost_gui.dir/export_file_loader.cc.o.d -o CMakeFiles/_ost_gui.dir/export_file_loader.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_file_loader.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o -MF CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o.d -o CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_file_viewer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/block_modifiers.hh:23, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_modeller.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_sip_handler.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:41, from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:38: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h:49: /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_modeller.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_perspective.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_main_area.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_scene_selection.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_panels.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_widget.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_widget.cc.o -MF CMakeFiles/_ost_gui.dir/export_widget.cc.o.d -o CMakeFiles/_ost_gui.dir/export_widget.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_widget.cc [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o -MF CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o.d -o CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_gl_canvas.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_selection.hh:23, from /build/openstructure-2.3.1/modules/gui/pymod/export_scene_selection.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o -MF CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o.d -o CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_menu_bar.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o -MF CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o.d -o CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_data_viewer.cc [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay.cc.o -MF CMakeFiles/_ost_gui.dir/export_overlay.cc.o.d -o CMakeFiles/_ost_gui.dir/export_overlay.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_overlay.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_file_viewer.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o -MF CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o.d -o CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o -c /build/openstructure-2.3.1/modules/gui/pymod/export_overlay_manager.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_file_loader.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:24, from /build/openstructure-2.3.1/modules/gui/pymod/export_file_loader.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_widget.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_gl_canvas.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/sip_handler.hh:22, from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:30, from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.cc:26: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gl_canvas.hh:23, from /build/openstructure-2.3.1/modules/gui/pymod/export_gl_canvas.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_overlay_manager.cc:16: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_overlay.cc:26: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/openstructure-2.3.1/modules/gui/pymod/export_data_viewer.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:35: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:33, from /build/openstructure-2.3.1/modules/gui/pymod/export_data_viewer.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:41: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qwidget.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QWidget:1, from /build/openstructure-2.3.1/modules/gui/pymod/sip_handler.hh:24: /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point_list.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh:28, from /build/openstructure-2.3.1/modules/gui/pymod/export_overlay.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/x86_64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QMainWindow:1, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main_window.hh:35: /usr/include/x86_64-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ [100%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/mol/mm/_ost_mol_mm.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol_mm.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/mol/mm/_ost_mol_mm.so CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol_mm.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libOpenMM.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/mm/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/mm/pymod/antechamber.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./antechamber.pyc\",\"antechamber.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] Built target _ost_mol_mm [100%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/gui/_ost_gui.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/presets.xml /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/scene/presets.xml cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/icons/color_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/scene/icons/color_icon.png cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/icons/preset_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/scene/icons/preset_icon.png cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/icons/render_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/scene/icons/render_icon.png cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/icons/tool_icon.png /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/share/openstructure/scene/icons/tool_icon.png cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_gui.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/gui/_ost_gui.so CMakeFiles/_ost_gui.dir/wrap_gui.cc.o CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o CMakeFiles/_ost_gui.dir/export_message_widget.cc.o CMakeFiles/_ost_gui.dir/export_gl_win.cc.o CMakeFiles/_ost_gui.dir/export_tool.cc.o CMakeFiles/_ost_gui.dir/export_py_shell.cc.o CMakeFiles/_ost_gui.dir/export_gosty.cc.o CMakeFiles/_ost_gui.dir/export_scene_win.cc.o CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o CMakeFiles/_ost_gui.dir/export_perspective.cc.o CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o CMakeFiles/_ost_gui.dir/export_main_area.cc.o CMakeFiles/_ost_gui.dir/export_panels.cc.o CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o CMakeFiles/_ost_gui.dir/export_file_loader.cc.o CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o CMakeFiles/_ost_gui.dir/export_widget.cc.o CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o CMakeFiles/_ost_gui.dir/export_overlay.cc.o CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_gui.so.2.3.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_gfx.so.2.3.1 /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/color_options_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_options_widget.pyc\",\"color_options_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/color_select_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_select_widget.pyc\",\"color_select_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/combo_options_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/combo_options_widget.pyc\",\"combo_options_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/cpk_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/cpk_widget.pyc\",\"cpk_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/custom_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/custom_widget.pyc\",\"custom_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_editor_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_editor_widget.pyc\",\"gradient_editor_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_info_handler.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_info_handler.pyc\",\"gradient_info_handler.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_list_model.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_list_model.pyc\",\"gradient_list_model.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_preset_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_preset_widget.pyc\",\"gradient_preset_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/hsc_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/hsc_widget.pyc\",\"hsc_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/immutable_gradient_info_handler.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_gradient_info_handler.pyc\",\"immutable_gradient_info_handler.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/immutable_preset_info_handler.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_preset_info_handler.pyc\",\"immutable_preset_info_handler.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/init_inspector.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/init_inspector.pyc\",\"init_inspector.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/inspector_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/inspector_widget.pyc\",\"inspector_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/map_level_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/map_level_widget.pyc\",\"map_level_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/preset.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset.pyc\",\"preset.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/remote.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/remote.pyc\",\"remote.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_list_model.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_list_model.pyc\",\"preset_editor_list_model.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_widget.pyc\",\"preset_editor_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/preset_info_handler.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_info_handler.pyc\",\"preset_info_handler.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/preset_list_model.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_list_model.pyc\",\"preset_list_model.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/preset_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_widget.pyc\",\"preset_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/render_mode_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_mode_widget.pyc\",\"render_mode_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/render_op.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_op.pyc\",\"render_op.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/render_options_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_options_widget.pyc\",\"render_options_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/scene_observer_impl.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_observer_impl.pyc\",\"scene_observer_impl.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/scene_selection_helper.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_selection_helper.pyc\",\"scene_selection_helper.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/simple_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/simple_widget.pyc\",\"simple_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/sline_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/sline_widget.pyc\",\"sline_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/toolbar_options_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/toolbar_options_widget.pyc\",\"toolbar_options_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/trace_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/trace_widget.pyc\",\"trace_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/tube_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/tube_widget.pyc\",\"tube_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/uniform_color_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/uniform_color_widget.pyc\",\"uniform_color_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/visibility_op.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/visibility_op.pyc\",\"visibility_op.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/line_trace_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/line_trace_widget.pyc\",\"line_trace_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/wireframe_widget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/wireframe_widget.pyc\",\"wireframe_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/query_editor.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/query_editor.pyc\",\"query_editor.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/dng/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/dng/termuse.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/termuse.pyc\",\"termuse.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/dng/superpositiondialog.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/superpositiondialog.pyc\",\"superpositiondialog.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/dng/init.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/init.pyc\",\"init.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/dng/menu.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/menu.pyc\",\"menu.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/init_context_menu.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_context_menu.pyc\",\"init_context_menu.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/init_menubar.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_menubar.pyc\",\"init_menubar.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/init_spacenav.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_spacenav.pyc\",\"init_spacenav.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/init_splash.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_splash.pyc\",\"init_splash.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/trajectory_viewer.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./trajectory_viewer.pyc\",\"trajectory_viewer.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/helpwidget.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./helpwidget.pyc\",\"helpwidget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/table.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./table.pyc\",\"table.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/gosty_startup.py\",\"/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./gosty_startup.pyc\",\"gosty_startup.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] Built target _ost_gui make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/ost_scripts.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_config /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost_config cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/bin/ost cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different dng /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/bin/dng cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_startup.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/ost_startup.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/scripts/dng_startup.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/dng_startup.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] Built target ost_scripts make[2]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/openstructure-2.3.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' dh_auto_test cd obj-x86_64-linux-gnu && make -j15 check ARGS\+=--verbose ARGS\+=-j15 make[1]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/openstructure-2.3.1 -B/build/openstructure-2.3.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 check make[2]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/openstructure-2.3.1 -B/build/openstructure-2.3.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/openstructure-2.3.1/obj-x86_64-linux-gnu/CMakeFiles 91 make -f CMakeFiles/Makefile2 CMakeFiles/check.dir/all make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_startup.py.dir/DependInfo.cmake --color= make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/create_stage.dir/DependInfo.cmake --color= make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_config.dir/DependInfo.cmake --color= make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake --color= make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/build make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/build make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost_config.in -DOUT_FILE=ost_config -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/ost.in -DOUT_FILE=ost -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/scripts/dng.in -DOUT_FILE=dng -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/openstructure-2.3.1/cmake_support/substitute.cmake make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/bin make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 0%] Built target subst_ost_startup.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec [ 0%] Built target subst_ost_config [ 0%] Built target subst_ost [ 0%] Built target subst_dng cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 0%] Built target create_stage make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/DependInfo.cmake --color= make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom_headers.dir/DependInfo.cmake --color= make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config_headers.dir/DependInfo.cmake --color= make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/ost_base_headers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src/CMakeFiles/ost_info_headers.dir/DependInfo.cmake --color= make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./alignment_opts.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./alignment_opts.hh make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/depend make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/DependInfo.cmake --color= make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/build make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/generic_property_def.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/generic_property_def.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/export_helper/vector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/export_helper/vector.hh make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/build make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./base.hh make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./clip_alignment.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info.hh make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/depend make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/DependInfo.cmake --color= make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/pair_to_tuple_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./conservation.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./conservation.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/pointer_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./def.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./def.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop_headers.dir/DependInfo.cmake --color= make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./config.hh make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src/CMakeFiles/ost_db_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_group.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/DependInfo.cmake --color= make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_error.hh make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/DependInfo.cmake --color= make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_prediction_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./exc.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./exc.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/vec_to_list_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/vec_to_list_conv.hh make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./dllexport.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./dllexport.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./conop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./conop.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/depend make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src/CMakeFiles/ost_io_headers.dir/DependInfo.cmake --color= make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_wrap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen.hh make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/test_utils/compare_files.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/test_utils/compare_files.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./version.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./version.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./geom.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./geom.hh make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./anisotropic.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./anisotropic.hh make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./processor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./processor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl_fw.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_conv.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_conv.hh make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./distance_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./generic_property.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./generic_property.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./amino_acids.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./amino_acids.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/dispatch.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/dispatch.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./auto_correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./entropy.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./entropy.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_option_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./module_config.hh make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./diag.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./diag.hh [ 0%] Built target ost_config_headers make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./svd_superpose.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./svd_superpose.hh make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./integrity_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./integrity_error.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat2.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_group.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./global_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./global_align.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./linear_indexer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./linear_indexer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/star_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/star_parser.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./model_check.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./model_check.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./clear.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clear.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_spec.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./invalid_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./invalid_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/src/./wrap_tmalign.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/bindings/./wrap_tmalign.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat3.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_item.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_item.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./ins_del.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./heuristic.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./heuristic.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./binary_container.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./binary_container.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./clip_min_max.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./sec_structure_segments.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./ptr_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./ptr_observer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat4.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat4.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./local_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./local_align.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./conjugate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./conjugate.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./log.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_list.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./extract_data_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/db/./extract_data_helper.hh [ 0%] Built target ost_bindings_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./local_dist_diff_test.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./local_dist_diff_test.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./merge_pairwise_alignments.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound_lib.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/io_profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./convolute.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./convolute.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log_sink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./log_sink.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/dihedral.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_def.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_path.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_path.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./distance_test_common.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./profile.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./correlate.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./forcefield.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./forcefield.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_option.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec2.hh [ 0%] Built target ost_db_headers make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./rule_based.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./rule_based.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./alignment_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./alignment_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./distance_rmsd_test.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_rmsd_test.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./minimal_compound_lib.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_set.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_set.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_factory.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./cross_correlate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./cross_correlate.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./ff_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./ff_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec3.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pqr_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound_lib_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./dyn_cast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./dyn_cast.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./module_config.hh make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_visitor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./semiglobal_align.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/config/CMakeFiles/ost_config.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./superpose_frames.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./density_slice.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./density_slice.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./buildingblock.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./buildingblock.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./ring_finder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./ring_finder.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_frequency_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mae_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec4.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec4.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./stdint.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./stdint.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./filter_clashes.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./block_modifiers.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_verbose_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh [ 0%] Built target ost_config cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./dft.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./dft.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./sequence_identity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_identity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/manipulator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./stdint_msc.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./stdint_msc.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./item_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_region.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_region.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./construct_cbeta.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fft.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fft.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./gromacs_block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./gromacs_block_modifiers.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh [ 0%] Built target ost_conop_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./sequence_similarity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat2_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./geom_info_conversion.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_column.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./clash_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./heuristic_block_modifiers.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./heuristic_block_modifiers.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fftw_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fftw_helper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./range.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./range.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_spatial_domain.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./item_type_cast.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type_cast.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_column_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat3_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./interaction.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./interaction.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fill.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fill.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./trajectory_analysis.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./variance_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./settings.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./settings.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./invalid_sequence.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat4_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/map_tool.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./structure_analysis.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./units.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./units.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pdb_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./filter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./filter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./views_from_sequences.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./simulation.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./simulation.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh [ 0%] Built target ost_info_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./circular_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./circular_iterator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./message.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./message.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./modeller.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./modeller.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./constants.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./constants.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fourier_filters.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./profile_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./profile_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./pdbize.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_pseudo_counts.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_row.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./platform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./platform.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./observer.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_gradient_magnitude.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/index.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/index.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_score.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./adjacency_bitmap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./state_extractor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./state_extractor.hh [ 0%] Built target ost_seq_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite2.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./string_ref.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./string_ref.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/type_fw.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./system_creator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./system_creator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite3.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./pod_vector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./pod_vector.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/save_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/save_entity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_laplacian.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh [ 0%] Built target ost_seq_alg_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/value_holder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/value_holder.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./contact_overlap.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology_creator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology_creator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/painter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./fixed_string.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./fixed_string.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./highest_peak_search_3d.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/secstr_row.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_entity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./algorithm.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./domain_find.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./index.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./index.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite2_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./tri_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./tri_matrix.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./histogram.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./histogram.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_secstr_painter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./circle_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./circle_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./similarity_matrix.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./line_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite3_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_selection_painter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_view.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_surface.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./boost_filesystem_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./composite_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./composite_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./steep.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./steep.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./local_sigma_threshold.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./aligned_cuboid.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./accessibility.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./accessibility.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_text_painter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./paged_array.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/./paged_array.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/tabulated_trig.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_algorithm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_algorithm.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./mask_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./mask_image.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec_mat_predicates.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_observer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_table.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_table.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./sec_struct.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_struct.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 0%] Built target ost_mol_mm_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./quat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./quat.hh [ 0%] Built target ost_base_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_types.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_types.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./negate.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./negate.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_model.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./nonstandard.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./nonstandard.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./transform.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer_factory.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./molck.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./molck.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_row.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/omf.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./debug.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./debug.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./point_cloud.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./point_cloud.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/custom_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/custom_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./find_membrane.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_view.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/load_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/load_map.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./dllexport.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./dllexport.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_iterator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_iterator.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./entity_to_density.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cpk_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_table_view.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_type.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_linear.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_class.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_class.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/image_format.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/image_format.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_log.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_log.hh [ 0%] Built target ost_geom_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/sline_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent.hh [ 0%] Built target ost_mol_alg_headers make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/tick_painter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_type.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_type.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_od.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_od.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_trace_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_factory.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_factory.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/title_row.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_group.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_group.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cartoon_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./power_spectrum.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_source.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/alignment_view_object.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./randomize.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./randomize.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./in_mem_coord_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./in_mem_coord_source.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/trace_render_options.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle_fw.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_view_object.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./smooth_mask_image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_frame.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_frame.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/geom/src/CMakeFiles/ost_geom.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_view_object.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh [ 2%] Built target ost_geom make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/ost_base.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_accumulator.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/main_thread_runner.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_list.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/pymod/CMakeFiles/_ost_geom.dir/DependInfo.cmake --color= make -f modules/geom/tests/CMakeFiles/ost_geom_tests.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_min_max.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests/CMakeFiles/ost_geom_tests.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./mol.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./mol.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./threshold.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./threshold.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/completer_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/completer_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/geom/tests/CMakeFiles/ost_geom_tests.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests.dir/build make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/base/src/CMakeFiles/ost_base.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh [ 2%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o [ 2%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_composite3.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/gutter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh [ 2%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_mat2.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transcendentals.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh [ 3%] Built target ost_base cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_mat3.cc make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/src/CMakeFiles/ost_info.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./inverted_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./inverted_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/path_completer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh [ 3%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/basic_gradient_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_composite2.cc [ 3%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./map.hh [ 3%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op2.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transform_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_context_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_mat4.cc [ 3%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op3.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_op2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_op2.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_op2.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_op3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_op3.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_op3.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_transform.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_completer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_property_mapper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/tiff_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_mirror.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_mirror.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_pass.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_pass.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_view.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/jpk_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/jpk_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_shift.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_op.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./bitmap_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./discrete_shrink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor.hh make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_visitor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./collada_exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformation_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/info/src/CMakeFiles/ost_info.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./color.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformations.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformations.hh [ 4%] Built target ost_info cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./handle_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./ics_editor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./ics_editor.hh [ 4%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op4.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op4.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_op4.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_op4.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_op4.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fractional_shift.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fractional_shift.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity_fw.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/geom/pymod/CMakeFiles/_ost_geom.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./not_connected_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./not_connected_error.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_tokenizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_tokenizer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_helper.hh [ 6%] Built target _ost_geom cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./property_id.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./property_id.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./polar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./polar.hh make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_impl.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/_ost_base.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./line_average.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_average.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_syntax_highlighter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/hhm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/hhm_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./rscrosscorr.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./rscrosscorr.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./null_data.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./null_data.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/pssm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pssm_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_error.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_error.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./observable.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./observable.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_state.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh [ 6%] Built target ost_img_alg_headers make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./paste_impl.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./paste_impl.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_base.hh [ 6%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_quat.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_quat.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_quat.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_quat.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_quat.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/load.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/load.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/base/pymod/CMakeFiles/_ost_base.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_visitor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_text_document_layout.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/save.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/save.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh [ 6%] Built target _ost_base cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/shell_history.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object.hh [ 7%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./binary_data_sink.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_sink.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_prop.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_vec2.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/state_machine.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./peak.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./peak.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/state.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_manager.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_view.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_view.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./phase.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./phase.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/transition.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./binary_data_source.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_source.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_prim.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./physical_units.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./physical_units.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./sec_structure.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./sec_structure.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./symmetry_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./pixel_sampling.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./pixel_sampling.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/button_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_test_object.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./spatial_organizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./container_serialization.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./container_serialization.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./point_list.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/drop_box.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glwin_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glwin_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./swap_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./swap_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./point.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./input.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./input.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_builder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_builder.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_utils.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_utils.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./polygon_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./polygon_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_manager.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./prim_list.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./prim_list.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./builder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./builder.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_exception.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_exception.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./progress.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./progress.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/bottom_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/bottom_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/button_box.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_box.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./size.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./size.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./convert.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./convert.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./selection.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./selection.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/event_button.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/event_button.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./converting_streams.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./converting_streams.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_prop.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./spherical_mask.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./spherical_mask.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./surface.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.cc /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./util.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./torsion_handle.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./torsion_handle.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_widget_container.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_widget_container.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./texture.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./texture.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./formatted_line.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./formatted_line.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar_widget_holder.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./chemdict_parser.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transfer_connectivity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./transfer_connectivity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/side_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/side_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/star_parser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./star_parser.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array_helper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_view_wrapper.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_view_wrapper.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./value_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./value_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/splitter_panel_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/splitter_panel_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene_observer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./vecmat.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./vecmat.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/tabbed_panel_bar.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_include.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_include.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_info_convert.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_info_convert.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_type_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_type_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/context_menu.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glext_include.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glext_include.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_info.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_info.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/current_selection_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_mode.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_mode.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/io_profile.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_profile.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/custom_part_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./xcs_editor.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./xcs_editor.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./material.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./material.hh [ 7%] Built target ost_img_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/dcd_io.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./dcd_io.hh make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bounding_box.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bounding_box.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_crd_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_part_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transform.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./transform.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/gfx_scene_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./module_config.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pqr_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./primitives.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./primitives.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/label_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/label_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray_fw.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mae_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/root_node.hh make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter.hh [ 7%] Built target ost_mol_headers make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/info/pymod/CMakeFiles/_ost_info.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_mode_node.hh make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh [ 7%] Built target _ost_info make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_modes_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gost_exporter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_node.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_slab.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_slab.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pdb_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso_prop.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/message_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_widget.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_writer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_sdf_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_box_widget.hh [ 7%] Built target ost_gfx_headers cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_writer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_writer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/save_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./save_entity.hh [ 7%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/log_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/log_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_vec3.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/load_entity.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_entity.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/argand.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/argand.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/load_surface.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_surface.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_msms_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_str.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_str.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/draw_overlay.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/drawing_functions.hh make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/omf.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./omf.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/fft_panel.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/info_panel.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/img2qt.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pir_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/mask_overlay.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/img/base/src/CMakeFiles/ost_img.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./promod_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/null_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/null_overlay.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./profile_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay.hh [ 10%] Built target ost_img make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/hhm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/pssm_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/clustal_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./clustal_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/load.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/save.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./save.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/load_map.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_map.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_df3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_df3_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_gui.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_gui.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/image_format.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./image_format.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_observer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_observer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dx_handler.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/base/src/CMakeFiles/ost_mol.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_spi_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_spi_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay_base.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay_base.hh [ 16%] Built target ost_mol make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_situs_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_situs_handler.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies_fw.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies_fw.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_mrc_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_mrc_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/viewer_normalizer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_browser.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_browser.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dat_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_ipl_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_ipl_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_type_dialog.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_type_dialog.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_jpk_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_jpk_handler.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_viewer.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_viewer.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_nanoscope_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gl_canvas.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_canvas.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dm3_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gl_win.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_win.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/build cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./scene_menu.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_menu.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_tiff_handler.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/tiff_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./tiff_util.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gosty_app.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gosty_app.hh [ 20%] Built target ost_img_alg make -f modules/base/tests/CMakeFiles/ost_base_tests.dir/build.make modules/base/tests/CMakeFiles/ost_base_tests.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/img/base/pymod/CMakeFiles/_ost_img.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/ost_base_tests.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/jpk_util.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/./jpk_util.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/base/tests/CMakeFiles/ost_base_tests.dir/build.make modules/base/tests/CMakeFiles/ost_base_tests.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./admin.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./admin.hh [ 20%] Built target ost_io_headers make -f modules/img/base/tests/CMakeFiles/ost_img_tests.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests.dir/depend cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./module_config.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./module_config.hh [ 20%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o -MF CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o.d -o CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o -c /build/openstructure-2.3.1/modules/base/tests/test_generic_property.cc [ 21%] Built target _ost_img make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests/CMakeFiles/ost_img_tests.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/base/tests/CMakeFiles/ost_img_tests.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main_area.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_area.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./perspective.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./perspective.hh [ 23%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_data.cc.o [ 23%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_data.cc.o -MF CMakeFiles/ost_img_tests.dir/test_data.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_data.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_data.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./scene_selection.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_selection.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_clear.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main_window.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_window.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./thin_splitter.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./thin_splitter.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_geom_handler.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_geom_handler.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_pool.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_pool.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_registry.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_registry.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_state_saver.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_state_saver.hh cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_loader.hh /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_loader.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 23%] Built target ost_gui_headers make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 23%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_atom_groups.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_op4.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_quat.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_mat4.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_mat3.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_mat2.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_composite2.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_composite3.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_op3.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/modules/geom/tests/test_composite3.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_vec3.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_op2.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_vec2.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/modules/img/base/tests/test_data.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/img/base/tests/test_data.hh:29, from /build/openstructure-2.3.1/modules/img/base/tests/test_data.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_atom_groups.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/base/tests/test_atom_groups.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_clear.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/alg/tests/test_clear.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/base/tests/test_generic_property.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/base/tests/test_generic_property.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_extent.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_extent.cc.o -MF CMakeFiles/ost_img_tests.dir/test_extent.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_extent.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_extent.cc [ 23%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_vec4.cc [ 23%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_transform.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_transform.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_transform.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_transform.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/test_transform.cc [ 23%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/tests.cc.o -MF CMakeFiles/ost_geom_tests.dir/tests.cc.o.d -o CMakeFiles/ost_geom_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/geom/tests/tests.cc [ 23%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image.cc.o -MF CMakeFiles/ost_img_tests.dir/test_image.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_image.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_image.cc [ 23%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_conj.cc [ 23%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state.cc.o -MF CMakeFiles/ost_img_tests.dir/test_image_state.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_image_state.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_image_state.cc [ 23%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_chain.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_chain.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_chain.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_chain.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc [ 23%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_convolute.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_vec4.cc:20: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_conn.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_conn.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_conn.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_conn.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_conn.cc [ 23%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_coord_group.cc [ 23%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_builder.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_builder.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_builder.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_builder.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_builder.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/tests/test_extent.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/base/tests/test_extent.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_delete.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_delete.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_delete.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_delete.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_delete.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_transform.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/geom/tests/test_transform.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/base/tests/test_image.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/base/tests/test_image.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_conj.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/alg/tests/test_conj.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_entity.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_entity.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_entity.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_entity.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc [ 23%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o -MF CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o.d -o CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o -c /build/openstructure-2.3.1/modules/base/tests/test_string_ref.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state.cc:32: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/builder.hh:26, from /build/openstructure-2.3.1/modules/mol/base/tests/test_builder.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/builder.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_conn.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/base/tests/test_conn.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_discrete_shrink.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_coord_group.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/base/tests/test_coord_group.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_convolute.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/alg/tests/test_convolute.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_delete.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/base/tests/test_delete.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_fft.cc [ 23%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o -MF CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.cc [ 23%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_fill.cc [ 23%] Linking CXX executable ../../../tests/ost_geom_tests cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_geom_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o CMakeFiles/ost_geom_tests.dir/test_op2.cc.o CMakeFiles/ost_geom_tests.dir/test_op3.cc.o CMakeFiles/ost_geom_tests.dir/test_op4.cc.o CMakeFiles/ost_geom_tests.dir/test_quat.cc.o CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o CMakeFiles/ost_geom_tests.dir/test_transform.cc.o CMakeFiles/ost_geom_tests.dir/tests.cc.o -o ../../../tests/ost_geom_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 23%] Built target ost_geom_tests make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/seq/base/src/CMakeFiles/ost_seq.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 24%] Built target ost_seq make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 26%] Built target _ost_mol make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/src/CMakeFiles/ost_db.dir/DependInfo.cmake --color= [ 26%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_filter.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/build In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec_mat_predicates.hh:28, from /build/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/db/src/CMakeFiles/ost_db.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 26%] Built target ost_db make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 27%] Built target _ost_img_alg make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings.dir/DependInfo.cmake --color= In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_discrete_shrink.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/alg/tests/test_discrete_shrink.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/bindings/src/CMakeFiles/ost_bindings.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 27%] Built target ost_bindings make -f modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 27%] running checks for module geom cd /build/openstructure-2.3.1/modules/geom/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_geom_tests Running 25 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 27%] Built target ost_geom_tests_run make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 27%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_sequence.cc [ 28%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_ics.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_ics.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_ics.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_ics.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_ics.cc [ 28%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_index.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_index.cc.o -MF CMakeFiles/ost_img_tests.dir/test_index.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_index.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_index.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_fill.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/alg/tests/test_fill.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_query.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_query.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_query.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_query.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/tests/test_fft.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/modules/img/alg/tests/test_fft.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_surface.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_surface.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_surface.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_surface.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_surface.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.hh:29, from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_residue.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_residue.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_residue.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_residue.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_residue.cc [ 28%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_histogram.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_filter.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/img/alg/tests/test_filter.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_ics.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/base/tests/test_ics.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/seq/base/tests/test_sequence.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/seq/base/tests/test_sequence.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_mirror.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o -MF CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o.d -o CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o -c /build/openstructure-2.3.1/modules/base/tests/test_pod_vector.cc [ 29%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_point.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_point.cc.o -MF CMakeFiles/ost_img_tests.dir/test_point.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_point.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_point.cc [ 29%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_sampling.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_sampling.cc.o -MF CMakeFiles/ost_img_tests.dir/test_sampling.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_sampling.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_sampling.cc [ 29%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_domains.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_domains.cc.o -MF CMakeFiles/ost_img_tests.dir/test_domains.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_domains.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_domains.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/histogram.hh:30, from /build/openstructure-2.3.1/modules/img/alg/tests/test_histogram.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/alg/tests/test_histogram.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_residue.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/base/tests/test_residue.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/openstructure-2.3.1/modules/mol/base/tests/test_surface.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/base/tests/test_surface.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_mirror.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/alg/tests/test_mirror.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/tests/test_point.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/img/base/tests/test_point.hh:29, from /build/openstructure-2.3.1/modules/img/base/tests/test_point.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh:31, from /build/openstructure-2.3.1/modules/img/base/tests/test_domains.cc:31: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/openstructure-2.3.1/modules/img/base/tests/test_domains.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/modules/img/base/tests/test_sampling.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/img/base/tests/test_sampling.hh:29, from /build/openstructure-2.3.1/modules/img/base/tests/test_sampling.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_negate.cc [ 29%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_view.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_view.cc [ 29%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/tests.cc.o -MF CMakeFiles/ost_base_tests.dir/tests.cc.o.d -o CMakeFiles/ost_base_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/base/tests/tests.cc [ 29%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_power_spectrum.cc [ 29%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_size.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_size.cc.o -MF CMakeFiles/ost_img_tests.dir/test_size.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_size.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_size.cc [ 29%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_transfer_connectivity.cc [ 29%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_shift.cc [ 29%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_view_op.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_negate.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/alg/tests/test_negate.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Linking CXX executable ../../../tests/ost_base_tests cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_base_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o CMakeFiles/ost_base_tests.dir/tests.cc.o -o ../../../tests/ost_base_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_view.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/base/tests/test_view.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 29%] Built target ost_base_tests [ 29%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/tests.cc.o -MF CMakeFiles/ost_mol_tests.dir/tests.cc.o.d -o CMakeFiles/ost_mol_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/tests.cc [ 30%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o -MF CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_value_holder.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_power_spectrum.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/alg/tests/test_power_spectrum.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/builder.hh:26, from /build/openstructure-2.3.1/modules/mol/base/tests/test_transfer_connectivity.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/builder.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:53: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void mol_base::throw_invalid_chain_handle::test_method()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In member function 'void mol_base::throw_invalid_chain_handle::test_method()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/string:40: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void mol_base::throw_invalid_chain_handle::test_method()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function 'void mol_base::throw_invalid_chain_handle::test_method()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void mol_base::throw_invalid_chain_handle::test_method()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void mol_base::throw_invalid_chain_handle::test_method()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void mol_base::throw_invalid_chain_handle::test_method()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void mol_base::throw_invalid_chain_handle::test_method()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 30%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc [ 30%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/tests.cc.o -MF CMakeFiles/ost_img_tests.dir/tests.cc.o.d -o CMakeFiles/ost_img_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/tests.cc In file included from /usr/include/c++/12/string:53: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ChainBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:36:21: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/string:40: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ChainBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:36:21: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ChainBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:36:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ChainBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:36:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:38:19: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:38:19: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:38:19: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:38:19: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:40:18: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:40:18: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:40:18: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:40:18: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 30%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_stat.cc [ 30%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_transform.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_shift.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/alg/tests/test_shift.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/test_normalizer.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_view_op.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/base/tests/test_view_op.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc [ 30%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/tests.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/img/alg/tests/tests.cc [ 30%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc [ 30%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_profile.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_profile.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_profile.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_profile.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_profile.cc [ 31%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/tests.cc.o -MF CMakeFiles/ost_seq_tests.dir/tests.cc.o.d -o CMakeFiles/ost_seq_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/tests.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_transform.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/alg/tests/test_transform.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/DependInfo.cmake --color= In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 32%] Built target ost_seq_alg make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Built target _ost_seq make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop.dir/DependInfo.cmake --color= In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/alg/tests/test_stat.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_normalizer.cc:35: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/openstructure-2.3.1/modules/img/alg/tests/test_normalizer.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Linking CXX executable ../../../../tests/ost_img_tests cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_img_tests.dir/test_data.cc.o CMakeFiles/ost_img_tests.dir/test_extent.cc.o CMakeFiles/ost_img_tests.dir/test_image.cc.o CMakeFiles/ost_img_tests.dir/test_image_state.cc.o CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o CMakeFiles/ost_img_tests.dir/test_index.cc.o CMakeFiles/ost_img_tests.dir/test_point.cc.o CMakeFiles/ost_img_tests.dir/test_sampling.cc.o CMakeFiles/ost_img_tests.dir/test_domains.cc.o CMakeFiles/ost_img_tests.dir/test_size.cc.o CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o CMakeFiles/ost_img_tests.dir/tests.cc.o -o ../../../../tests/ost_img_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/gfx/src/CMakeFiles/ost_gfx.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 41%] Built target ost_gfx make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/pymod/CMakeFiles/_ost_conop.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/build [ 41%] Built target ost_img_tests make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/conop/pymod/CMakeFiles/_ost_conop.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 42%] Built target _ost_conop make -f modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 42%] running checks for module img cd /build/openstructure-2.3.1/modules/img/base/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_img_tests Running 44 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 42%] Built target ost_img_tests_run [ 42%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o -MF CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o.d -o CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o -c /build/openstructure-2.3.1/modules/conop/tests/test_heuristic_conop.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/DependInfo.cmake --color= [ 45%] Built target ost_mol_alg make -f modules/io/src/CMakeFiles/ost_io.dir/build.make modules/io/src/CMakeFiles/ost_io.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/src/CMakeFiles/ost_io.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 47%] Built target _ost_gfx make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 48%] Built target _ost_mol_alg [ 48%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/tests.cc.o -MF CMakeFiles/ost_conop_tests.dir/tests.cc.o.d -o CMakeFiles/ost_conop_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/conop/tests/tests.cc [ 48%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o -MF CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o.d -o CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o -c /build/openstructure-2.3.1/modules/conop/tests/test_rule_based_conop.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/io/src/CMakeFiles/ost_io.dir/build.make modules/io/src/CMakeFiles/ost_io.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/io/src/CMakeFiles/ost_io.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 52%] Built target ost_io make -f modules/gui/src/CMakeFiles/ost_gui.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/depend In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui.dir/DependInfo.cmake --color= In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/io/pymod/CMakeFiles/_ost_io.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 53%] Built target _ost_io make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 53%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/tests.cc.o -MF CMakeFiles/ost_gfx_tests.dir/tests.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/gfx/tests/tests.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/conop/tests/test_amino_acids.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/openstructure-2.3.1/modules/conop/tests/test_heuristic_conop.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/conop/tests/test_rule_based_conop.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/conop/tests/test_rule_based_conop.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o -MF CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o -c /build/openstructure-2.3.1/modules/gfx/tests/test_gfx_node.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, from /build/openstructure-2.3.1/modules/mol/alg/tests/test_superposition.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_crd.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh:25, from /build/openstructure-2.3.1/modules/io/tests/test_clustal.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/io/tests/test_clustal.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/conop/tests/helper.cc:3: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/conop/tests/helper.cc:2: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/tests/tests.cc [ 89%] Linking CXX executable ../../../../tests/ost_img_alg_tests cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img_alg_tests.dir/link.txt --verbose=1 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec_mat_predicates.hh:28, from /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -o ../../../../tests/ost_img_alg_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gfx/tests/test_gfx_node.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:26, from /build/openstructure-2.3.1/modules/gfx/tests/test_gfx_node.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 89%] Built target ost_img_alg_tests make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 90%] Built target ost_mol_mm make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/_ost_gui.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 90%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/build In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc:33: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/gui/pymod/CMakeFiles/_ost_gui.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 92%] Built target _ost_gui make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 92%] running checks for module img_alg cd /build/openstructure-2.3.1/modules/img/alg/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_img_alg_tests Running 25 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 92%] Built target ost_img_alg_tests_run [ 92%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/tests/test_merge_pairwise_alignments.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/io/tests/test_io_crd.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/io/tests/test_io_crd.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 92%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/tests/test_consistency_checks.cc [ 92%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -c /build/openstructure-2.3.1/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc [ 92%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_dcd.cc [ 92%] Linking CXX executable ../../../../tests/ost_seq_tests cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o CMakeFiles/ost_seq_tests.dir/test_profile.cc.o CMakeFiles/ost_seq_tests.dir/tests.cc.o -o ../../../../tests/ost_seq_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 92%] Built target ost_seq_tests make -f modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/build.make modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/build.make modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 92%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_interaction.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc:28: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/clip_alignment.hh:27, from /build/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc:30: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 92%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_block.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/merge_pairwise_alignments.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/tests/test_merge_pairwise_alignments.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/seq/alg/tests/test_merge_pairwise_alignments.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 92%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_block_modifiers.cc make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] Built target _ost_mol_mm make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/tests/test_consistency_checks.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/alg/tests/test_consistency_checks.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 93%] running checks for module seq cd /build/openstructure-2.3.1/modules/seq/base/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_seq_tests Running 32 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] Built target ost_seq_tests_run make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/ost_scripts.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_config /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost_config [ 93%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/bin/ost cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different dng /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/bin/dng cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_startup.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/ost_startup.py cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/scripts/dng_startup.py /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/dng_startup.py make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] Built target ost_scripts make -f modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] running checks test_aaindex.py cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_aaindex.py" . ---------------------------------------------------------------------- Ran 1 test in 0.615s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] Built target test_aaindex.py_run make -f modules/base/tests/CMakeFiles/test_stutil.py_run.dir/build.make modules/base/tests/CMakeFiles/test_stutil.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/test_stutil.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/base/tests/CMakeFiles/test_stutil.py_run.dir/build.make modules/base/tests/CMakeFiles/test_stutil.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] running checks test_stutil.py cd /build/openstructure-2.3.1/modules/base/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/base/tests/test_stutil.py" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, from /build/openstructure-2.3.1/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ ...... ---------------------------------------------------------------------- Ran 6 tests in 0.004s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] Built target test_stutil.py_run make -f modules/base/tests/CMakeFiles/test_table.py_run.dir/build.make modules/base/tests/CMakeFiles/test_table.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/test_table.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/base/tests/CMakeFiles/test_table.py_run.dir/build.make modules/base/tests/CMakeFiles/test_table.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] running checks test_table.py cd /build/openstructure-2.3.1/modules/base/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/base/tests/test_table.py" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_group.hh:29, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh:28, from /build/openstructure-2.3.1/modules/io/tests/test_io_dcd.cc:23: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/io/tests/test_io_dcd.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 93%] Linking CXX executable ../../../../tests/ost_mol_tests cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o CMakeFiles/ost_mol_tests.dir/test_chain.cc.o CMakeFiles/ost_mol_tests.dir/test_conn.cc.o CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o CMakeFiles/ost_mol_tests.dir/test_builder.cc.o CMakeFiles/ost_mol_tests.dir/test_delete.cc.o CMakeFiles/ost_mol_tests.dir/test_entity.cc.o CMakeFiles/ost_mol_tests.dir/test_ics.cc.o CMakeFiles/ost_mol_tests.dir/test_query.cc.o CMakeFiles/ost_mol_tests.dir/test_surface.cc.o CMakeFiles/ost_mol_tests.dir/test_residue.cc.o CMakeFiles/ost_mol_tests.dir/test_view.cc.o CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o CMakeFiles/ost_mol_tests.dir/tests.cc.o -o ../../../../tests/ost_mol_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 .......................make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] Built target ost_mol_tests make -f modules/base/tests/CMakeFiles/test_log.py_run.dir/build.make modules/base/tests/CMakeFiles/test_log.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/test_log.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/base/tests/CMakeFiles/test_log.py_run.dir/build.make modules/base/tests/CMakeFiles/test_log.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] running checks test_log.py cd /build/openstructure-2.3.1/modules/base/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/base/tests/test_log.py" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_interaction.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_interaction.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ .... ---------------------------------------------------------------------- Ran 4 tests in 0.014s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] Built target test_log.py_run make -f modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' ...........[ 93%] running checks test_msms.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_msms.py" ....In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_block_modifiers.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_block_modifiers.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/lib/python3.11/unittest/case.py:579: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/enrichment-out.png'> if method() is not None: ResourceWarning: Enable tracemalloc to get the object allocation traceback .[ 93%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_color.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_color.cc.o -MF CMakeFiles/ost_gfx_tests.dir/test_color.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/test_color.cc.o -c /build/openstructure-2.3.1/modules/gfx/tests/test_color.cc [ 93%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_sdf.cc Could not find msms executable: ignoring unit tests [ 93%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_sequence_profile.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] Built target test_msms.py_run make -f modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' .[ 93%] running checks test_clustalw.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_clustalw.py" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_block.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_block.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/lib/python3.11/unittest/case.py:579: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/roc-out.png'> if method() is not None: ResourceWarning: Enable tracemalloc to get the object allocation traceback .In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/lib/python3.11/unittest/case.py:579: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/roc-same-val-out.png'> if method() is not None: ResourceWarning: Enable tracemalloc to get the object allocation traceback ................../build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ost/table.py:2186: DeprecationWarning: scipy.isnan is deprecated and will be removed in SciPy 2.0.0, use numpy.isnan instead if scipy.isnan(correl): ......................... ---------------------------------------------------------------------- Ran 83 tests in 11.018s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] Built target test_table.py_run make -f modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] running checks test_hhblits.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_hhblits.py" No HHblits installation found: skip unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] Built target test_hhblits.py_run make -f modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] running checks test_blast.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_blast.py" .Could not find blast executable: ignoring unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' .[ 93%] Built target test_blast.py_run make -f modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] running checks test_kclust.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_kclust.py" .... ---------------------------------------------------------------------- Ran 7 tests in 6.761s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 93%] Built target test_clustalw.py_run make -f modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/DependInfo.cmake --color= In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/tests/test_color.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/iterator:61, from /usr/include/boost/operators.hpp:98, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/build Could not find kClust executable: ignoring unit tests make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 94%] running checks test_naccess.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_naccess.py" make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 94%] Built target test_kclust.py_run make -f modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 94%] running checks test_cadscore.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_cadscore.py" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ Could not find NACCESS, could not test binding... [ 94%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_pir.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_pir.cc.o -MF CMakeFiles/ost_io_tests.dir/test_pir.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_pir.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_pir.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 94%] Built target test_naccess.py_run make -f modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/DependInfo.cmake --color= [ 94%] Linking CXX executable ../../../../tests/ost_mol_alg_tests cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_alg_tests.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/build /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -o ../../../../tests/ost_mol_alg_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 94%] running checks test_tmtools.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_tmtools.py" ... ---------------------------------------------------------------------- Ran 2 tests in 0.236s OK Could not find tmalign executable: ignoring unit tests Could not find tmalign executable: ignoring unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 94%] Built target test_tmtools.py_run make -f modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 94%] running checks test_ialign.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_ialign.py" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/load.hh:27, from /build/openstructure-2.3.1/modules/io/tests/test_io_sequence_profile.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/io/tests/test_io_sequence_profile.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 94%] Built target ost_mol_alg_tests make -f modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 94%] running checks test_lga.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_lga.py" [ 95%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/tests/test_sequence_identity.cc . ---------------------------------------------------------------------- Ran 1 test in 0.185s OK Could not find ialign master perl script: ignoring unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 95%] Built target test_ialign.py_run make -f modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 95%] running checks test_hbplus.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_hbplus.py" . ---------------------------------------------------------------------- Ran 1 test in 0.181s OK Could not find lga executable: ignoring unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 95%] Built target test_lga.py_run make -f modules/conop/tests/CMakeFiles/test_processor.py_run.dir/build.make modules/conop/tests/CMakeFiles/test_processor.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests/CMakeFiles/test_processor.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/conop/tests/CMakeFiles/test_processor.py_run.dir/build.make modules/conop/tests/CMakeFiles/test_processor.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 95%] running checks test_processor.py cd /build/openstructure-2.3.1/modules/conop/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/conop/tests/test_processor.py" Could not find hbplus, could not test binding... . ---------------------------------------------------------------------- Ran 1 test in 0.009s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 95%] Built target test_processor.py_run make -f modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/build.make modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/depend make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/build.make modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 95%] Built target test_hbplus.py_run make -f modules/geom/tests/CMakeFiles/test_geom.py_run.dir/build.make modules/geom/tests/CMakeFiles/test_geom.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/geom/tests/CMakeFiles/test_geom.py_run.dir/DependInfo.cmake --color= [ 95%] running checks test_linear_db.py cd /build/openstructure-2.3.1/modules/db/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/db/tests/test_linear_db.py" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/geom/tests/CMakeFiles/test_geom.py_run.dir/build.make modules/geom/tests/CMakeFiles/test_geom.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 95%] running checks test_geom.py cd /build/openstructure-2.3.1/modules/geom/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/geom/tests/test_geom.py" ... ---------------------------------------------------------------------- Ran 3 tests in 0.051s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' ....[ 95%] Built target test_linear_db.py_run .... ---------------------------------------------------------------------- Ran 8 tests in 0.100s OK [ 95%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/tests/tests.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 95%] Built target test_geom.py_run make -f modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/build.make modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/build.make modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_gfx.py cd /build/openstructure-2.3.1/modules/gfx/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/gfx/tests/test_gfx.py" ...... ---------------------------------------------------------------------- Ran 6 tests in 0.029s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target test_gfx.py_run make -f modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_io_pdb.py cd /build/openstructure-2.3.1/modules/io/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.py" ...s ---------------------------------------------------------------------- Ran 4 tests in 0.033s OK (skipped=1) make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target test_io_pdb.py_run make -f modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_io_mmcif.py cd /build/openstructure-2.3.1/modules/io/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/io/tests/test_io_mmcif.py" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/io/tests/test_io_sdf.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/io/tests/test_io_sdf.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ .In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh:25, from /build/openstructure-2.3.1/modules/io/tests/test_pir.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/io/tests/test_pir.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ .[ 96%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -MF CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -c /build/openstructure-2.3.1/modules/gfx/tests/test_map_octree.cc .......s ---------------------------------------------------------------------- Ran 10 tests in 6.106s OK (skipped=1) [ 96%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_forcefield.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target test_io_mmcif.py_run make -f modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_io_omf.py cd /build/openstructure-2.3.1/modules/io/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/io/tests/test_io_omf.py" In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/sequence_identity.hh:26, from /build/openstructure-2.3.1/modules/seq/alg/tests/test_sequence_identity.cc:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/seq/alg/tests/test_sequence_identity.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build .make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' ---------------------------------------------------------------------- Ran 1 test in 3.282s OK [ 96%] running checks for module mol cd /build/openstructure-2.3.1/modules/mol/base/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_mol_tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target test_io_omf.py_run make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' Running 70 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks for module mol_alg cd /build/openstructure-2.3.1/modules/mol/alg/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_mol_alg_tests [ 96%] Built target ost_mol_tests_run make -f modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_pdbize.py cd /build/openstructure-2.3.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/alg/tests/test_pdbize.py" Running 4 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target ost_mol_alg_tests_run make -f modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_convenient_superpose.py cd /build/openstructure-2.3.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/alg/tests/test_convenient_superpose.py" ........ ---------------------------------------------------------------------- Ran 8 tests in 0.038s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target test_pdbize.py_run make -f modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_hbond.py cd /build/openstructure-2.3.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/alg/tests/test_hbond.py" ... ---------------------------------------------------------------------- Ran 2 tests in 0.069s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target test_hbond.py_run make -f modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_accessibility.py cd /build/openstructure-2.3.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/alg/tests/test_accessibility.py" [ 96%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc .smake -f modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_sec_struct.py cd /build/openstructure-2.3.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/alg/tests/test_sec_struct.py" .s ---------------------------------------------------------------------- Ran 1 test in 0.000s OK (skipped=1) make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target test_sec_struct.py_run make -f modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/build.make modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/DependInfo.cmake --color= .make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/build.make modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_antechamber.py cd /build/openstructure-2.3.1/modules/mol/mm/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/mol/mm/tests/test_antechamber.py" .... ---------------------------------------------------------------------- Ran 3 tests in 0.262s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target test_antechamber.py_run make -f modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/build.make modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/depend In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh:22, from /build/openstructure-2.3.1/modules/gfx/tests/test_map_octree.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:32: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/build.make modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_seq.py cd /build/openstructure-2.3.1/modules/seq/base/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/base/tests/test_seq.py" ................ ---------------------------------------------------------------------- Ran 14 tests in 0.049s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target test_seq.py_run make -f modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_renumber.py cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_renumber.py" .In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_forcefield.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_forcefield.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ . ---------------------------------------------------------------------- Ran 9 tests in 10.537s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target test_convenient_superpose.py_run make -f modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_local_align.py cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_local_align.py" ........ ---------------------------------------------------------------------- Ran 8 tests in 0.251s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target test_renumber.py_run make -f modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_global_align.py cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_global_align.py" ... ---------------------------------------------------------------------- Ran 3 tests in 0.002s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target test_local_align.py_run make -f modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_semiglobal_align.py cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_semiglobal_align.py" ... ---------------------------------------------------------------------- Ran 3 tests in 0.002s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target test_global_align.py_run make -f modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/DependInfo.cmake --color= . ---------------------------------------------------------------------- Ran 1 test in 0.006s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_weight_matrix.py cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_weight_matrix.py" make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target test_semiglobal_align.py_run make -f modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] running checks test_alignment_from_chain_view.py cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_alignment_from_chain_view.py" . ---------------------------------------------------------------------- Ran 1 test in 0.015s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 96%] Built target test_alignment_from_chain_view.py_run [ 96%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o -MF CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_iomanager.cc .. ---------------------------------------------------------------------- Ran 2 tests in 0.000s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 97%] Linking CXX executable ../../../tests/ost_conop_tests [ 97%] Built target test_weight_matrix.py_run cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_conop_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o CMakeFiles/ost_conop_tests.dir/tests.cc.o CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o CMakeFiles/ost_conop_tests.dir/helper.cc.o -o ../../../tests/ost_conop_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so [ 98%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/tests.cc [ 98%] Linking CXX executable ../../../../tests/ost_seq_alg_tests cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_alg_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -o ../../../../tests/ost_seq_alg_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so [ 98%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/tests.cc.o -MF CMakeFiles/ost_io_tests.dir/tests.cc.o.d -o CMakeFiles/ost_io_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/io/tests/tests.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 98%] Built target ost_conop_tests make -f modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 98%] running checks for module conop cd /build/openstructure-2.3.1/modules/conop/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_conop_tests Running 16 test cases... unable to open database file unable to open database file unable to open database file unable to open database file unable to open database file unable to open database file unable to open database file unable to open database file *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 98%] Built target ost_conop_tests_run [ 98%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o -MF CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_star_parser.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc:21: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 98%] Built target ost_seq_alg_tests make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 98%] running checks for module seq_alg cd /build/openstructure-2.3.1/modules/seq/alg/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_seq_alg_tests Running 19 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [ 98%] Built target ost_seq_alg_tests_run [100%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o -MF CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_mmcif_reader.cc . ---------------------------------------------------------------------- Ran 2 tests in 19.938s OK (skipped=1) Could not find NACCESS, could not compare Accessiblity function... make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] Built target test_accessibility.py_run [100%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o -MF CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_mmcif_info.cc [100%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_img.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_img.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_img.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_img.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_io_img.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [100%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o -MF CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o -c /build/openstructure-2.3.1/modules/io/tests/test_exceptions.cc In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh:25, from /build/openstructure-2.3.1/modules/io/tests/test_mmcif_info.cc:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/io/tests/test_mmcif_info.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/tests/test_iomanager.cc:22: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/io/tests/test_iomanager.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [100%] Linking CXX executable ../../../tests/ost_gfx_tests cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gfx_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_gfx_tests.dir/tests.cc.o CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o CMakeFiles/ost_gfx_tests.dir/test_color.cc.o CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -o ../../../tests/ost_gfx_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_gfx.so.2.3.1 ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] Built target ost_gfx_tests make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] running checks for module gfx cd /build/openstructure-2.3.1/modules/gfx/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_gfx_tests Running 13 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] Built target ost_gfx_tests_run In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/load_map.hh:24, from /build/openstructure-2.3.1/modules/io/tests/test_io_img.cc:29: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/io/tests/test_io_img.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:24, from /build/openstructure-2.3.1/modules/io/tests/test_mmcif_reader.cc:26: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/io/tests/test_mmcif_reader.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/io/tests/test_star_parser.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/io/tests/test_star_parser.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/load_map.hh:24, from /build/openstructure-2.3.1/modules/io/tests/test_exceptions.cc:27: /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/openstructure-2.3.1/modules/io/tests/test_exceptions.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ . ---------------------------------------------------------------------- Ran 2 tests in 133.069s OK Could not find CAD score classic executables: ignoring unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] Built target test_cadscore.py_run [100%] Linking CXX executable ../../../../tests/ost_mol_mm_tests cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_mm_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o -o ../../../../tests/ost_mol_mm_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_mol_mm.so.2.3.1 ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libOpenMM.so make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] Built target ost_mol_mm_tests make -f modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests_run.dir/build.make modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests_run.dir/build.make modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] running checks for module mol_mm cd /build/openstructure-2.3.1/modules/mol/mm/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_mol_mm_tests Running 13 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] Built target ost_mol_mm_tests_run [100%] Linking CXX executable ../../../tests/ost_io_tests cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_io_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_io_tests.dir/test_clustal.cc.o CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o CMakeFiles/ost_io_tests.dir/test_pir.cc.o CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o CMakeFiles/ost_io_tests.dir/tests.cc.o CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o CMakeFiles/ost_io_tests.dir/test_io_img.cc.o CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o -o ../../../tests/ost_io_tests -L/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_io.so.2.3.1 ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_thread.so /usr/lib/x86_64-linux-gnu/libboost_chrono.so /usr/lib/x86_64-linux-gnu/libboost_date_time.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] Built target ost_io_tests make -f modules/io/tests/CMakeFiles/ost_io_tests_run.dir/build.make modules/io/tests/CMakeFiles/ost_io_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/ost_io_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f modules/io/tests/CMakeFiles/ost_io_tests_run.dir/build.make modules/io/tests/CMakeFiles/ost_io_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] running checks for module io cd /build/openstructure-2.3.1/modules/io/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-x86_64-linux-gnu/stage /build/openstructure-2.3.1/obj-x86_64-linux-gnu/tests/ost_io_tests Running 159 test cases... unable to open database file WARNING: skipping SEQRES import unit test. Compound lib is required unable to open database file WARNING: skipping mmcif_convert_seqres unit test. Compound library is required unable to open database file WARNING: skipping mmcif_entity_poly_tests unit test. Compound library is required unable to open database file *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] Built target ost_io_tests_run make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' cd /build/openstructure-2.3.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1 /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu /build/openstructure-2.3.1/obj-x86_64-linux-gnu/CMakeFiles/check.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'CMakeFiles/check.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' [100%] Built target check make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/openstructure-2.3.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/openstructure-2.3.1' dh_auto_install cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/openstructure-2.3.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/openstructure-2.3.1 -B/build/openstructure-2.3.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_base.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_base.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_base.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_base.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/export_helper/generic_property_def.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/export_helper/pair_to_tuple_conv.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/export_helper/vec_to_list_conv.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/test_utils/compare_files.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./generic_property.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./integrity_error.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./invalid_handle.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./ptr_observer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./log.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./log_sink.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./profile.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./dyn_cast.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./stdint.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./stdint_msc.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./range.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./module_config.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./units.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./message.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./platform.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./string_ref.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./pod_vector.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./fixed_string.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./tri_matrix.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./boost_filesystem_helper.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./paged_array.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/_ost_base.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/_ost_base.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/./settings.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/./stutil.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/./table.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/./table_selector.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/./xmlrunner.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/./testutils.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/./settings.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/./stutil.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/./table.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/./table_selector.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/./xmlrunner.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/./testutils.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_bindings.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_bindings.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_bindings.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_bindings.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/bindings/./wrap_tmalign.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/_ost_bindings.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/_ost_bindings.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./lga.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./hbplus.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./msms.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./tmtools.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./dssp.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./clustalw.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./utils.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./naccess.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./hhblits.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./hhblits2.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./hhblits3.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./blast.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./cadscore.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./kclust.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./ialign.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./mmseqs2.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./lga.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./hbplus.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./msms.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./tmtools.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./dssp.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./clustalw.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./utils.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./naccess.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./hhblits.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./hhblits2.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./hhblits3.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./blast.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./cadscore.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./kclust.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./ialign.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/bindings/./mmseqs2.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./config.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./dllexport.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/./version.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_conop.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_conop.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_conop.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_conop.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/conop/./conop.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/conop/./processor.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/conop/./amino_acids.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/conop/./diag.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/conop/./model_check.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/conop/./heuristic.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/conop/./compound.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/conop/./compound_lib.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/conop/./module_config.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/conop/./rule_based.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/conop/./minimal_compound_lib.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/conop/./compound_lib_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/conop/./ring_finder.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/bin/chemdict_tool -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/bin/chemdict_tool" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/conop/_ost_conop.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/conop/_ost_conop.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/conop/./__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/conop/./cleanup.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/conop/./__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/conop/./cleanup.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_db.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_db.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_db.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_db.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/db/./sqlite_wrap.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/db/./sqlite_conv.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/db/./module_config.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/db/./linear_indexer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/db/./binary_container.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/db/./extract_data_helper.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/db/_ost_db.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/db/_ost_db.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/db/./__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/db/./__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_geom.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_geom.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_geom.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_geom.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/export_helper/vector.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./def.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./exc.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./geom.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./mat.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./mat2.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./mat3.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./mat4.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./vec.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./vec2.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./vec3.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./vec4.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./vecmat_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./vecmat2_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./vecmat3_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./vecmat4_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./circular_iterator.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./constants.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./composite.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./composite2.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./composite3.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./composite_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./composite2_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./composite3_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./aligned_cuboid.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./vec_mat_predicates.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./quat.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./transform.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./point_cloud.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/geom/./module_config.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/geom/_ost_geom.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/geom/_ost_geom.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/geom/./__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/geom/./__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_gfx.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_gfx.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_gfx.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_gfx.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/map_iso_gen.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/map_iso_gen_s.hh -- Up-to-date: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/map_iso_gen_s.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/map_iso_spec.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/map_octree.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/octree_isocont.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/cartoon_renderer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/custom_renderer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/cpk_renderer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/debug_renderer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/simple_renderer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/sline_renderer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/trace_renderer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/line_trace_renderer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/backbone_trace.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/entity_detail.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/entity_renderer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/trace_renderer_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/connect_renderer_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/mapped_property.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/entity_renderer_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/tabulated_trig.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/impl/fast_spheres.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/render_options/render_options.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/render_options/line_render_options.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/render_options/custom_render_options.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/render_options/cpk_render_options.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/render_options/simple_render_options.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/render_options/sline_render_options.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/render_options/line_trace_render_options.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/render_options/cartoon_render_options.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/render_options/trace_render_options.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/color_ops/color_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/color_ops/by_element_color_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/color_ops/by_chain_color_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/color_ops/uniform_color_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/color_ops/gradient_color_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/color_ops/entity_view_color_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/color_ops/basic_gradient_color_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/color_ops/gradient_level_color_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/color_ops/map_handle_color_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./render_pass.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./bitmap_io.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./collada_exporter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./color.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./entity.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./entity_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./gl_helper.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./gfx.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./gfx_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./gfx_node.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./gfx_node_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./gfx_node_visitor.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./gfx_object_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./gfx_object.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./gfx_object_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./gfx_prim.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./symmetry_node.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./gfx_test_object.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./glwin_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./input.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./prim_list.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./scene.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./selection.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./surface.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./texture.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./vertex_array.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./vertex_array_helper.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./scene_observer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./gl_include.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./glext_include.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./render_mode.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./material.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./gradient.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./gradient_manager.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./module_config.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./primitives.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./povray_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./povray.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./exporter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./exporter_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./gost_exporter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./map_handle_color_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./map_iso.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./map_slab.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gfx/./map_iso_prop.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/textures/test_texture.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/textures/glyph_texture.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gfx/_ost_gfx.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gfx/_ost_gfx.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gfx/./__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gfx/./py_gfx_obj.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gfx/./__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gfx/./py_gfx_obj.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/scene/gradients.xml -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_gui.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_gui.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_gui.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_gui.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/tools/tool.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/tools/tool_option_group.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/tools/tool_options.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/tools/tool_bar.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/tools/selection_tool.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/tools/measure_tool.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/tools/tool_option.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/tools/tool_manager.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/tools/tool_options_widget.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/tools/manipulator.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/tools/tool_options_win.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/tools/mouse_event.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/tools/map_tool.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/align_properties_painter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/base_row.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/background_painter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/conservation_painter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/painter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/secstr_row.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/seq_secstr_painter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/seq_selection_painter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/seq_text_painter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/sequence_delegate.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/sequence_model.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/sequence_row.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/sequence_search_bar.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/sequence_table_view.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/sequence_viewer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/tick_painter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/title_row.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/alignment_view_object.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/base_view_object.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/sequence_viewer/sequence_view_object.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/main_thread_runner.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/output_redirector.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/completer_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/dir_model.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/gutter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/path_completer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/python_context_parser.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/python_completer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/python_shell.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/python_shell_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/python_shell_widget.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/python_tokenizer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/python_syntax_highlighter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/text_logger.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/python_interpreter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/python_interpreter_worker.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/python_shell_text_document_layout.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/shell_history.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/state_machine.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/state.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/transition.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/python_shell/transition_guard.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/panels/button_bar.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/panels/drop_box.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/panels/panel_bar.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/panels/panel_manager.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/panels/bottom_bar.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/panels/button_box.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/panels/event_button.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/panels/panel_widget_container.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/panels/panel_bar_widget_holder.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/panels/side_bar.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/panels/splitter_panel_bar.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/panels/tabbed_panel_bar.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/scene_win/context_menu.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/scene_win/current_selection_node.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/scene_win/custom_part_node.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/scene_win/entity_node.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/scene_win/entity_part_node.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/scene_win/gfx_scene_node.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/scene_win/label_node.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/scene_win/root_node.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/scene_win/render_mode_node.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/scene_win/render_modes_node.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/scene_win/scene_node.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/scene_win/scene_win.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/scene_win/scene_win_model.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/messages/message_widget.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/messages/message_box_widget.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/messages/log_reader.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/argand.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/data_viewer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/data_viewer_panel.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/data_viewer_panel_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/draw_overlay.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/drawing_functions.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/fft_panel.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/info_panel.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/img2qt.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/mask_overlay.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/null_overlay.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/overlay.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/overlay_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/overlay_base_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/overlay_manager.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/overlay_manager_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/overlay_manager_gui.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/overlay_manager_observer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/pointlist_overlay.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/pointlist_overlay_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/strategies.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/strategies_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/data_viewer/viewer_normalizer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./file_browser.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./file_type_dialog.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./file_viewer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./gl_canvas.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./gl_win.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./scene_menu.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./gosty_app.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./admin.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./module_config.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./main.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./main_area.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./perspective.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./scene_selection.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./main_window.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./dock_widget.hh -- Up-to-date: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./dock_widget.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./thin_splitter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./widget.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./widget_geom_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./widget_pool.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./widget_registry.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./widget_state_saver.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/gui/./file_loader.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/openstructure/libexec/gosty -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/openstructure/libexec/gosty" to "$ORIGIN/../../lib" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/add_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/close_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/critical_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/delete_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/distance_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/find_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/information_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/map_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/menubar_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/rigid_body_manipulator_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/selection_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/show_sidebar_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/site_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/split_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/warning_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/icons/refresh.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/gui/images/logo-small.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/_ost_gui.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/_ost_gui.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/color_options_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/color_select_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/combo_options_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/cpk_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/custom_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/gradient_editor_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/gradient_info_handler.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/gradient_list_model.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/gradient_preset_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/hsc_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/immutable_gradient_info_handler.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/immutable_preset_info_handler.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/init_inspector.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/inspector_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/map_level_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/preset.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/remote.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/preset_editor_list_model.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/preset_editor_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/preset_info_handler.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/preset_list_model.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/preset_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/render_mode_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/render_op.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/render_options_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/scene_observer_impl.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/scene_selection_helper.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/simple_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/sline_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/toolbar_options_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/trace_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/tube_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/uniform_color_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/visibility_op.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/line_trace_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/wireframe_widget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/query_editor.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/color_options_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/color_select_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/combo_options_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/cpk_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/custom_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/gradient_editor_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/gradient_info_handler.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/gradient_list_model.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/gradient_preset_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/hsc_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/immutable_gradient_info_handler.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/immutable_preset_info_handler.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/init_inspector.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/inspector_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/map_level_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/preset.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/remote.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/preset_editor_list_model.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/preset_editor_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/preset_info_handler.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/preset_list_model.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/preset_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/render_mode_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/render_op.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/render_options_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/scene_observer_impl.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/scene_selection_helper.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/simple_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/sline_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/toolbar_options_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/trace_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/tube_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/uniform_color_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/visibility_op.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/line_trace_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/wireframe_widget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/scene/query_editor.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/dng/__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/dng/termuse.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/dng/superpositiondialog.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/dng/init.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/dng/menu.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/dng/__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/dng/termuse.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/dng/superpositiondialog.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/dng/init.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/dng/menu.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./init_context_menu.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./init_menubar.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./init_spacenav.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./init_splash.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./trajectory_viewer.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./helpwidget.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./table.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./gosty_startup.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./init_context_menu.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./init_menubar.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./init_spacenav.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./init_splash.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./trajectory_viewer.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./helpwidget.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./table.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/gui/./gosty_startup.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/scene/presets.xml -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/scene/icons/color_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/scene/icons/preset_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/scene/icons/render_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/scene/icons/tool_icon.png -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_img.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_img.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_img.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_img.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/raster_image/raster_image.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/dispatch.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/image_state.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/image_state_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/image_state_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/image_state_base_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/image_state_def.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/image_state_factory.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/image_state_frequency_domain.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/image_state_half_frequency_domain.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/image_state_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/image_state_spatial_domain.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/image_state_visitor.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/image_state_algorithm.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/image_state_visitor_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/index.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/type_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/image_state/value_holder.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./algorithm.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./circle_mask.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./composite_mask.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./data_algorithm.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./data_observer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./data_types.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./data.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./debug.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./dllexport.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./extent_iterator.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./extent_mask.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./extent.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./image_factory.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./image_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./image_handle_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./image_handle.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./image_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./image_list.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./image_state_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./image_state.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./image.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./inverted_mask.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./map.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./mask_base_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./mask_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./mask_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./mask_visitor.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./mask.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./module_config.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./normalizer_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./normalizer_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./null_data.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./observable.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./paste_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./peak.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./phase.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./physical_units.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./pixel_sampling.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./point_list.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./point.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./polygon_mask.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./progress.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./size.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./spherical_mask.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./util.cc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./util.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./value_util.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./vecmat.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/./mask_info_convert.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/img/_ost_img.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/img/_ost_img.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/img/./__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/img/./__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_img_alg.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_img_alg.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_img_alg.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_img_alg.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./anisotropic.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./auto_correlate.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./clear.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./clip_min_max.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./conjugate.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./convolute.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./correlate.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./cross_correlate.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./density_slice.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./dft.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./fft.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./fftw_helper.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./fill.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./filter.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./fourier_filters.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./gaussian_gradient_magnitude.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./gaussian.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./gaussian_laplacian.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./highest_peak_search_3d.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./histogram.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./line_iterator.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./local_sigma_threshold.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./mask_image.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./negate.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./normalizer_factory.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./norm.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./normalizer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./norm_linear.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./norm_log.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./norm_od.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./power_spectrum.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./randomize.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./smooth_mask_image.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./stat.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./stat_accumulator.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./stat_min_max.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./threshold.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./transcendentals.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./transform.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./transform_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./alg_transform.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./alg_mirror.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./alg_shift.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./discrete_shrink.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./transformation_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./transformations.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./fractional_shift.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./module_config.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./polar.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./line_average.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/img/alg/./rscrosscorr.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/img/alg/_ost_img_alg.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/img/alg/_ost_img_alg.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/img/alg/./__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/img/alg/./__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_info.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_info.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_info.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_info.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./info.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./info_error.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./info_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./info_impl_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./info_handle.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./info_group.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./info_item.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./info_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./module_config.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./info_path.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./info_set.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./info_visitor.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./info_verbose_visitor.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./item_type.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./geom_info_conversion.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/info/./item_type_cast.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/info/_ost_info.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/info/_ost_info.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/info/./__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/info/./__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_io.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_io.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_io.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_io.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/chemdict_parser.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/star_parser.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/mmcif_reader.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/mmcif_info.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/io_profile.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/dcd_io.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/entity_io_crd_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/entity_io_pqr_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/entity_io_mae_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/entity_io_mmcif_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/entity_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/pdb_reader.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/entity_io_pdb_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/pdb_writer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/entity_io_sdf_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/sdf_reader.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/sdf_writer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/save_entity.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/load_entity.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/surface_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/load_surface.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/surface_io_msms_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/pdb_str.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/stereochemical_params_reader.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/mol/omf.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/load_map.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/map_io_df3_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/image_format.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/map_io_dx_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/map_io_spi_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/map_io_situs_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/map_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/map_io_mrc_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/map_io_dat_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/map_io_ipl_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/map_io_jpk_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/map_io_nanoscope_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/map_io_png_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/map_io_dm3_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/map_io_tiff_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/tiff_util.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/img/jpk_util.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/seq/sequence_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/seq/fasta_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/seq/pir_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/seq/promod_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/seq/profile_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/seq/hhm_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/seq/pssm_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/seq/clustal_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/seq/load.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/seq/save.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./binary_data_sink.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./io_manager.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./binary_data_source.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./module_config.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./container_serialization.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./swap_util.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./io_utils.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./io_exception.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./convert.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./converting_streams.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./formatted_line.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./chemdict_parser.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./star_parser.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./mmcif_reader.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./mmcif_info.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./io_profile.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./dcd_io.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./entity_io_crd_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./entity_io_pqr_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./entity_io_mae_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./entity_io_mmcif_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./entity_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./pdb_reader.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./entity_io_pdb_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./pdb_writer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./entity_io_sdf_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./sdf_reader.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./sdf_writer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./save_entity.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./load_entity.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./surface_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./load_surface.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./surface_io_msms_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./pdb_str.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./stereochemical_params_reader.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./omf.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./sequence_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./fasta_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./pir_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./promod_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./profile_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./hhm_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./pssm_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./clustal_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./load.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./save.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./load_map.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./map_io_df3_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./image_format.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./map_io_dx_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./map_io_spi_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./map_io_situs_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./map_io_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./map_io_mrc_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./map_io_dat_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./map_io_ipl_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./map_io_jpk_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./map_io_nanoscope_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./map_io_png_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./map_io_dm3_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./map_io_tiff_handler.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./tiff_util.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/io/./jpk_util.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/io/_ost_io.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/io/_ost_io.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/io/./__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/io/./remote.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/io/./repository.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/io/./__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/io/./remote.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/io/./repository.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_mol.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_mol.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_mol.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_mol.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/pointer_iterator.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/atom_group.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/atom_prop.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/atom_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/atom_impl_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/chain_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/chain_impl_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/connector_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/connector_impl_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/dihedral.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/entity_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/entity_impl_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/fragment_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/fragment_impl_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/query_ast.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/query_ast_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/query_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/query_impl_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/residue_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/residue_impl_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/surface_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/surface_impl_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/torsion_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/impl/torsion_impl_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./atom_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./atom_handle.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./atom_view.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./bond_handle.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./bond_table.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./chain_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./chain_handle.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./chain_view.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./chain_type.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./chem_class.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./chem_type.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./coord_group.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./coord_source.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./in_mem_coord_source.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./coord_frame.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./editor_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./editor_type_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./mol.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./entity_base.hh -- Up-to-date: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./entity_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./entity_handle.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./entity_observer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./entity_observer_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./entity_property_mapper.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./entity_view.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./entity_visitor.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./entity_visitor_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./handle_type_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./ics_editor.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./not_connected_error.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./property_id.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./query.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./query_error.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./query_state.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./residue_base.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./residue_handle.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./residue_prop.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./residue_view.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./sec_structure.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./spatial_organizer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./surface.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./surface_builder.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./builder.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./surface_handle.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./surface_prop.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./torsion_handle.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./transfer_connectivity.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./query_view_wrapper.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./view_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./view_type_fw.hh -- Up-to-date: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./view_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./xcs_editor.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./bounding_box.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./transform.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/./module_config.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/_ost_mol.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/_ost_mol.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/./__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/./__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/bin/lddt -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/bin/lddt" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_mol_alg.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_mol_alg.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_mol_alg.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_mol_alg.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./svd_superpose.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./module_config.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./sec_structure_segments.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./local_dist_diff_test.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./distance_test_common.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./distance_rmsd_test.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./superpose_frames.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./filter_clashes.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./construct_cbeta.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./clash_score.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./trajectory_analysis.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./structure_analysis.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./consistency_checks.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./pdbize.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./adjacency_bitmap.hh -- Up-to-date: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./consistency_checks.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./contact_overlap.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./domain_find.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./similarity_matrix.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./accessibility.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./sec_struct.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./nonstandard.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./molck.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./find_membrane.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/alg/./entity_to_density.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/atom_scattering_properties.txt -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/stereo_chemical_props.txt -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/_ost_mol_alg.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/_ost_mol_alg.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./views.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./superpose.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./qsscoring.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./trajectory_analysis.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./structure_analysis.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./helix_kinks.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./hbond.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./views.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./superpose.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./qsscoring.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./trajectory_analysis.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./structure_analysis.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./helix_kinks.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/alg/./hbond.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_mol_mm.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_mol_mm.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_mol_mm.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_mol_mm.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./forcefield.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./ff_reader.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./buildingblock.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./block_modifiers.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./gromacs_block_modifiers.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./heuristic_block_modifiers.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./interaction.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./settings.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./simulation.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./modeller.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./observer.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./state_extractor.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./system_creator.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./topology_creator.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./index.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./topology.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/mol/mm/./steep.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/forcefields/AMBER03.dat -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/forcefields/CHARMM27.dat -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/mm/_ost_mol_mm.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/mm/_ost_mol_mm.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/mm/./__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/mm/./antechamber.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/mm/./__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/mol/mm/./antechamber.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_seq.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_seq.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_seq.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_seq.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/impl/sequence_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/impl/sequence_impl_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/impl/sequence_list_impl_fw.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/impl/sequence_list_impl.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/impl/sequence_list_iterator.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/./sequence_list.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/./sequence_handle.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/./alignment_handle.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/./module_config.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/./sequence_op.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/./aligned_region.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/./aligned_column.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/./aligned_column_iterator.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/./invalid_sequence.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/./views_from_sequences.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/./profile_handle.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/seq/_ost_seq.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/seq/_ost_seq.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/seq/./__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/seq/./__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_seq_alg.so.2.3.1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_seq_alg.so.2.3 -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/libost_seq_alg.so.2.3.1" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/libost_seq_alg.so -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./alignment_opts.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./clip_alignment.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./conservation.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./contact_prediction_score.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./contact_weight_matrix.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./distance_map.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./entropy.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./global_align.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./ins_del.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./local_align.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./merge_pairwise_alignments.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./module_config.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./pair_subst_weight_matrix.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./semiglobal_align.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./sequence_identity.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./sequence_similarity.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./subst_weight_matrix.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./variance_map.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./default_contact_weight_matrix.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./hmm_pseudo_counts.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/include/ost/seq/alg/./hmm_score.hh -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/seq/alg/_ost_seq_alg.so -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/seq/alg/_ost_seq_alg.so" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/seq/alg/./__init__.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/seq/alg/./mat.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/seq/alg/./renumber.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/seq/alg/./aaindex.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/seq/alg/./__init__.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/seq/alg/./mat.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/seq/alg/./renumber.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/seq/alg/./aaindex.pyc -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/aaindex/aaindex1 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/aaindex/aaindex2 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/share/openstructure/aaindex/aaindex3 -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/openstructure/libexec/ost_config -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/bin/ost -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/bin/dng -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/ost_startup.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/python3.11/dist-packages/ost/dng_startup.py -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/bin/molck -- Set runtime path of "/build/openstructure-2.3.1/debian/tmp/usr/bin/molck" to "" -- Installing: /build/openstructure-2.3.1/debian/tmp/usr/lib/openstructure/libexec/ost-compare-structures make[2]: Leaving directory '/build/openstructure-2.3.1/obj-x86_64-linux-gnu' find debian/tmp/usr/lib -name '*.pyc' | xargs --no-run-if-empty rm make[1]: Leaving directory '/build/openstructure-2.3.1' debian/rules override_dh_install make[1]: Entering directory '/build/openstructure-2.3.1' dh_install find debian/python3-ost/usr/lib/python3/dist-packages -type f \ | xargs --no-run-if-empty chmod -x find debian/tmp/usr/lib -name 'libost_*.so.*' \ | while read LIB; \ do dh_install -p$(echo $LIB | cut -d / -f 5 | cut -d . -f 1 | sed 's/_/-/g')2.3 \ $LIB usr/lib/x86_64-linux-gnu; \ done find debian/tmp/usr/lib -name 'libost_*.so' \ | while read LIB; \ do dh_install -p$(echo $LIB | cut -d / -f 5 | cut -d . -f 1 | sed 's/_/-/g')-dev \ $LIB usr/lib/x86_64-linux-gnu; \ done make[1]: Leaving directory '/build/openstructure-2.3.1' dh_installdocs dh_installchangelogs dh_python3 I: dh_python3 fs:483: renaming _ost_base.so to _ost_base.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _ost_seq.so to _ost_seq.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _ost_seq_alg.so to _ost_seq_alg.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _ost_mol.so to _ost_mol.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _ost_mol_mm.so to _ost_mol_mm.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _ost_mol_alg.so to _ost_mol_alg.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _ost_io.so to _ost_io.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _ost_info.so to _ost_info.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _ost_img.so to _ost_img.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _ost_img_alg.so to _ost_img_alg.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _ost_gui.so to _ost_gui.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _ost_gfx.so to _ost_gfx.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _ost_geom.so to _ost_geom.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _ost_db.so to _ost_db.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _ost_conop.so to _ost_conop.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _ost_bindings.so to _ost_bindings.cpython-311-x86_64-linux-gnu.so dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Provides field of package python3-ost: substitution variable ${python3:Provides} used, but is not defined dpkg-gencontrol: warning: Provides field of package python3-ost: substitution variable ${python3:Provides} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'libost-base2.3' in '../libost-base2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-img2.3' in '../libost-img2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-geom2.3' in '../libost-geom2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-conop2.3' in '../libost-conop2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-gui2.3' in '../libost-gui2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'openstructure' in '../openstructure_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-io2.3' in '../libost-io2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-base-dev' in '../libost-base-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-mol-mm-dev' in '../libost-mol-mm-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-geom-dev' in '../libost-geom-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-img-dev' in '../libost-img-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-mol-mm2.3' in '../libost-mol-mm2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-seq-alg2.3' in '../libost-seq-alg2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-bindings-dev' in '../libost-bindings-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-gfx-dev' in '../libost-gfx-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-mol-dev' in '../libost-mol-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-base2.3-dbgsym' in '../libost-base2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-geom2.3-dbgsym' in '../libost-geom2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-conop-dev' in '../libost-conop-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-info-dev' in '../libost-info-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-db-dev' in '../libost-db-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-io-dev' in '../libost-io-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-bindings2.3' in '../libost-bindings2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-seq-alg-dev' in '../libost-seq-alg-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-bindings2.3-dbgsym' in '../libost-bindings2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-img2.3-dbgsym' in '../libost-img2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-mol-alg-dev' in '../libost-mol-alg-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-gui-dev' in '../libost-gui-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-conop2.3-dbgsym' in '../libost-conop2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-seq-alg2.3-dbgsym' in '../libost-seq-alg2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-mol-mm2.3-dbgsym' in '../libost-mol-mm2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-gfx2.3' in '../libost-gfx2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-img-alg-dev' in '../libost-img-alg-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-gui2.3-dbgsym' in '../libost-gui2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-info2.3' in '../libost-info2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-gfx2.3-dbgsym' in '../libost-gfx2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-info2.3-dbgsym' in '../libost-info2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-seq2.3' in '../libost-seq2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-seq-dev' in '../libost-seq-dev_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-io2.3-dbgsym' in '../libost-io2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-seq2.3-dbgsym' in '../libost-seq2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-db2.3' in '../libost-db2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-db2.3-dbgsym' in '../libost-db2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-mol2.3' in '../libost-mol2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-mol2.3-dbgsym' in '../libost-mol2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-mol-alg2.3' in '../libost-mol-alg2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-mol-alg2.3-dbgsym' in '../libost-mol-alg2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-img-alg2.3' in '../libost-img-alg2.3_2.3.1-9_amd64.deb'. dpkg-deb: building package 'libost-img-alg2.3-dbgsym' in '../libost-img-alg2.3-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'openstructure-dbgsym' in '../openstructure-dbgsym_2.3.1-9_amd64.deb'. dpkg-deb: building package 'python3-ost' in '../python3-ost_2.3.1-9_amd64.deb'. dpkg-deb: building package 'python3-ost-dbgsym' in '../python3-ost-dbgsym_2.3.1-9_amd64.deb'. dpkg-genbuildinfo --build=binary -O../openstructure_2.3.1-9_amd64.buildinfo dpkg-genchanges --build=binary -O../openstructure_2.3.1-9_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1244763/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1244763 and its subdirectories I: Current time: Sat Jun 3 21:59:42 +14 2023 I: pbuilder-time-stamp: 1685779182