I: pbuilder: network access will be disabled during build I: Current time: Sun Aug 3 00:28:15 -12 2025 I: pbuilder-time-stamp: 1754224095 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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_2.6.1-1~exp.dsc] I: copying [./openstructure_2.6.1.orig.tar.xz] I: copying [./openstructure_2.6.1-1~exp.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jan 26 09:47:55 2024 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_2.6.1-1~exp.dsc: no acceptable signature found dpkg-source: info: extracting openstructure in openstructure-2.6.1 dpkg-source: info: unpacking openstructure_2.6.1.orig.tar.xz dpkg-source: info: unpacking openstructure_2.6.1-1~exp.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 add-python3-shebangs.patch dpkg-source: info: applying ost_config.patch dpkg-source: info: applying skip-dssp-tests.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2221909/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='experimental' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ccc10840a6df43349415658d6e3170a5' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2221909' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.tHcWnG62/pbuilderrc_FUGm --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tHcWnG62/b1 --logfile b1/build.log openstructure_2.6.1-1~exp.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 5 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2221909/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, 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 ... 19685 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 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-dejavu-mono{a} fonts-lyx{a} gettext{a} gettext-base{a} gfortran-13{a} gfortran-13-x86-64-linux-gnu{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libarchive13t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblas3{a} libboost-all-dev{a} libboost-atomic-dev{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono-dev{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-container-dev{a} libboost-container1.83-dev{a} libboost-container1.83.0{a} libboost-context-dev{a} libboost-context1.83-dev{a} libboost-context1.83.0{a} libboost-coroutine-dev{a} libboost-coroutine1.83-dev{a} libboost-coroutine1.83.0{a} libboost-date-time-dev{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{a} libboost-dev{a} libboost-exception-dev{a} libboost-exception1.83-dev{a} libboost-fiber-dev{a} libboost-fiber1.83-dev{a} libboost-fiber1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-graph-dev{a} libboost-graph-parallel-dev{a} libboost-graph-parallel1.83-dev{a} libboost-graph-parallel1.83.0{a} libboost-graph1.83-dev{a} libboost-graph1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-json-dev{a} libboost-json1.83-dev{a} libboost-json1.83.0{a} libboost-locale-dev{a} libboost-locale1.83-dev{a} libboost-locale1.83.0{a} libboost-log-dev{a} libboost-log1.83-dev{a} libboost-log1.83.0{a} libboost-math-dev{a} libboost-math1.83-dev{a} libboost-math1.83.0{a} libboost-mpi-dev{a} libboost-mpi-python-dev{a} libboost-mpi-python1.83-dev{a} libboost-mpi-python1.83.0{a} libboost-mpi1.83-dev{a} libboost-mpi1.83.0{a} libboost-nowide-dev{a} libboost-nowide1.83-dev{a} libboost-nowide1.83.0{a} libboost-numpy-dev{a} libboost-numpy1.83-dev{a} libboost-numpy1.83.0{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-python-dev{a} libboost-python1.83-dev{a} libboost-python1.83.0{a} libboost-random-dev{a} libboost-random1.83-dev{a} libboost-random1.83.0{a} libboost-regex-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization-dev{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-stacktrace-dev{a} libboost-stacktrace1.83-dev{a} libboost-stacktrace1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-test-dev{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost-timer-dev{a} libboost-timer1.83-dev{a} libboost-timer1.83.0{a} libboost-tools-dev{a} libboost-type-erasure-dev{a} libboost-type-erasure1.83-dev{a} libboost-type-erasure1.83.0{a} libboost-url-dev{a} libboost-url1.83-dev{a} libboost-url1.83.0{a} libboost-wave-dev{a} libboost-wave1.83-dev{a} libboost-wave1.83.0{a} libboost1.83-dev{a} libboost1.83-tools-dev{a} libbrotli1{a} libcbor0.10{a} libcifpp-data{a} libcifpp5{a} libcom-err2{a} libcups2t64{a} libcurl4t64{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-radeon1{a} libdrm2{a} libedit2{a} libegl-dev{a} libegl-mesa0{a} libegl1{a} libeigen3-dev{a} libelf1t64{a} libevdev2{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{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-13-dev{a} libgfortran5{a} libgl-dev{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglu1-mesa{a} libglu1-mesa-dev{a} libglvnd0{a} libglx-dev{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgudev-1.0-0{a} libharfbuzz0b{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{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} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc-dev{a} liblerc4{a} libllvm17t64{a} libltdl-dev{a} libltdl7{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libmd4c0{a} libmtdev1t64{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} libopengl-dev{a} libopengl0{a} libopenjp2-7{a} libopenmm-dev{a} libopenmm-plugins{a} libopenmm8.1{a} libopenmpi-dev{a} libopenmpi3t64{a} libpciaccess0{a} libpcre2-16-0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libqhull-r8.0{a} libqt5concurrent5t64{a} libqt5core5t64{a} libqt5dbus5t64{a} libqt5designer5{a} libqt5gui5t64{a} libqt5help5{a} libqt5network5t64{a} libqt5opengl5-dev{a} libqt5opengl5t64{a} libqt5printsupport5t64{a} libqt5sql5t64{a} libqt5test5t64{a} libqt5widgets5t64{a} libqt5xml5t64{a} libraqm0{a} librdmacm1t64{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsharpyuv-dev{a} libsharpyuv0{a} libsm6{a} libsqlite3-dev{a} libssh2-1t64{a} libtcl8.6{a} libtiff-dev{a} libtiff6{a} libtiffxx6{a} libtk8.6{a} libtool{a} libuchardet0{a} libucx0{a} libuv1t64{a} libvulkan-dev{a} libvulkan1{a} libwacom-common{a} libwacom9{a} libwayland-client0{a} libwayland-server0{a} libwebp-dev{a} libwebp7{a} libwebpdecoder3{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} 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} netbase{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-appdirs{a} python3-attr{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-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-pyparsing{a} python3-pyqt5{a} python3-pyqt5.sip{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3-unicodedata2{a} python3.12{a} python3.12-dev{a} python3.12-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} tk8.6-blt2.5{a} tzdata{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 krb5-locales 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-cssselect python3-html5lib python3-olefile qt5-gtk-platformtheme qttranslations5-l10n qtwayland5 wget xauth xdg-user-dirs 0 packages upgraded, 442 newly installed, 0 to remove and 0 not upgraded. Need to get 304 MB of archives. After unpacking 1555 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.4-1 [811 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.4-1 [2136 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.2-1 [26.5 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.4-1 [1948 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.4-1 [664 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.2-1 [9432 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.2-1 [27.5 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-1 [199 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-9 [96.2 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-2 [1411 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-1.2 [28.2 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.15.0-1 [78.5 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.2-1 [32.2 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.2-1 [80.0 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 33 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.2-1 [324 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.2-1 [136 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:9.7p1-6 [965 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-1 [723 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get: 62 http://deb.debian.org/debian unstable/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3 [670 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.2-2.1 [346 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-1 [186 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.62.1-1 [75.5 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.8.0-1 [441 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-5 [148 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.29.6-1 [2168 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.29.6-1 [10.7 MB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.16 [88.6 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 85 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-1 [1593 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.16 [891 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-3.1 [77.7 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-3.1 [131 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libcifpp-data all 5.0.7.1-3 [452 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libcifpp5 amd64 5.0.7.1-3+b1 [870 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 dssp amd64 4.2.2-2 [624 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.0-1 [189 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.1.0-2 [837 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libgfortran-13-dev amd64 13.3.0-1 [847 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.3.0-1 [10.6 MB] Get: 104 http://deb.debian.org/debian unstable/main amd64 gfortran-13 amd64 13.3.0-1 [13.2 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 52.0-2 [61.6 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 52.0-2 [343 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-4+b1 [208 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-12+b1 [23.7 MB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.121-2 [7972 B] Get: 114 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.121-2 [38.3 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.121-2 [22.0 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-3 [10.6 MB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-3 [233 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-3 [235 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libboost-atomic-dev amd64 1.83.0.2+b2 [3904 B] Get: 129 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-3 [239 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83-dev amd64 1.83.0-3 [244 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libboost-chrono-dev amd64 1.83.0.2+b2 [4224 B] Get: 132 http://deb.debian.org/debian unstable/main amd64 libboost-container1.83.0 amd64 1.83.0-3 [258 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libboost-container1.83-dev amd64 1.83.0-3 [263 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libboost-container-dev amd64 1.83.0.2+b2 [4072 B] Get: 135 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83.0 amd64 1.83.0-3 [230 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83.0 amd64 1.83.0-3 [332 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83-dev amd64 1.83.0-3 [372 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83-dev amd64 1.83.0-3 [239 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-3 [230 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-3 [231 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83.0 amd64 1.83.0-3 [269 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83-dev amd64 1.83.0-3 [276 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libboost-context1.83.0 amd64 1.83.0-3 [231 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libboost-context1.83-dev amd64 1.83.0-3 [232 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libboost-context-dev amd64 1.83.0.2+b2 [3804 B] Get: 146 http://deb.debian.org/debian unstable/main amd64 libboost-coroutine1.83.0 amd64 1.83.0-3 [234 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libboost-coroutine1.83-dev amd64 1.83.0-3 [236 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libboost-coroutine-dev amd64 1.83.0.2+b2 [3868 B] Get: 149 http://deb.debian.org/debian unstable/main amd64 libboost-date-time-dev amd64 1.83.0.2+b2 [3596 B] Get: 150 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 151 http://deb.debian.org/debian unstable/main amd64 libboost-exception1.83-dev amd64 1.83.0-3 [230 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libboost-exception-dev amd64 1.83.0.2+b2 [3584 B] Get: 153 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-3 [280 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-3 [295 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libboost-fiber1.83.0 amd64 1.83.0-3 [253 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libboost-fiber1.83-dev amd64 1.83.0-3 [264 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libboost-fiber-dev amd64 1.83.0.2+b2 [4028 B] Get: 158 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get: 159 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83.0 amd64 1.83.0-3 [358 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-3 [324 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-4+b1 [10.4 MB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-3 [342 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83.0 amd64 1.83.0-3 [466 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83-dev amd64 1.83.0-3 [536 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83-dev amd64 1.83.0-3 [383 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libboost-graph-dev amd64 1.83.0.2+b2 [3700 B] Get: 167 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10 [131 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [53.9 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 52.0-2 [70.2 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.11.0-1 [162 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.11.0-1 [17.9 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 5.0.2-3 [652 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 52.0-2 [27.7 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 52.0-2 [43.3 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.17.0+ds-1 [1127 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libboost-mpi1.83.0 amd64 1.83.0-3 [271 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libboost-graph-parallel1.83.0 amd64 1.83.0-3 [279 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libboost-graph-parallel1.83-dev amd64 1.83.0-3 [283 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libboost-graph-parallel-dev amd64 1.83.0.2+b2 [3728 B] Get: 188 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-3 [260 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get: 190 http://deb.debian.org/debian unstable/main amd64 libboost-json1.83.0 amd64 1.83.0-3 [354 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libboost-json1.83-dev amd64 1.83.0-3 [369 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libboost-json-dev amd64 1.83.0.2+b2 [3704 B] Get: 193 http://deb.debian.org/debian unstable/main amd64 libboost-locale1.83.0 amd64 1.83.0-3 [464 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libboost-locale1.83-dev amd64 1.83.0-3 [548 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libboost-locale-dev amd64 1.83.0.2+b2 [3924 B] Get: 196 http://deb.debian.org/debian unstable/main amd64 libboost-log1.83.0 amd64 1.83.0-3 [700 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libboost-log1.83-dev amd64 1.83.0-3 [871 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libboost-log-dev amd64 1.83.0.2+b2 [3796 B] Get: 199 http://deb.debian.org/debian unstable/main amd64 libboost-math1.83.0 amd64 1.83.0-3 [506 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libboost-math1.83-dev amd64 1.83.0-3 [549 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libboost-math-dev amd64 1.83.0.2+b2 [3796 B] Get: 202 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 4.1.6-13.3 [169 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3 [99.4 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3 [199 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 52.0-2 [647 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1 [36.2 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.7-7+b1 [393 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.4.7-7+b1 [164 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.11.0-1 [251 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [181 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10 [107 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10 [60.8 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10 [305 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 5.0.2-3 [3940 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 4.1.6-13.3 [226 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 4.1.6-13.3 [972 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.15 [3152 B] Get: 221 http://deb.debian.org/debian unstable/main amd64 libboost-mpi1.83-dev amd64 1.83.0-3 [289 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libboost-mpi-dev amd64 1.83.0.2+b2 [3680 B] Get: 223 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83.0 amd64 1.83.0-3 [351 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 mpi-default-bin amd64 1.15 [2408 B] Get: 225 http://deb.debian.org/debian unstable/main amd64 libboost-mpi-python1.83.0 amd64 1.83.0-3 [435 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libboost-mpi-python1.83-dev amd64 1.83.0-3 [239 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libboost-mpi-python-dev amd64 1.83.0.2+b2 [3712 B] Get: 228 http://deb.debian.org/debian unstable/main amd64 libboost-nowide1.83.0 amd64 1.83.0-3 [234 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libboost-nowide1.83-dev amd64 1.83.0-3 [236 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libboost-nowide-dev amd64 1.83.0.2+b2 [3668 B] Get: 231 http://deb.debian.org/debian unstable/main amd64 libboost-numpy1.83.0 amd64 1.83.0-3 [247 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libboost-numpy1.83-dev amd64 1.83.0-3 [253 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libboost-numpy-dev amd64 1.83.0.2+b2 [3644 B] Get: 234 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-3 [345 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83-dev amd64 1.83.0-3 [373 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 237 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.4-1 [2111 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.4-1 [5067 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.2-1 [9680 B] Get: 241 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.4-1 [499 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.2.6-9 [150 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.2-1 [26.2 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83-dev amd64 1.83.0-3 [379 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Get: 247 http://deb.debian.org/debian unstable/main amd64 libboost-random1.83.0 amd64 1.83.0-3 [238 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libboost-random1.83-dev amd64 1.83.0-3 [240 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libboost-random-dev amd64 1.83.0.2+b2 [3592 B] Get: 250 http://deb.debian.org/debian unstable/main amd64 libboost-regex-dev amd64 1.83.0.2+b2 [3864 B] Get: 251 http://deb.debian.org/debian unstable/main amd64 libboost-serialization-dev amd64 1.83.0.2+b2 [3832 B] Get: 252 http://deb.debian.org/debian unstable/main amd64 libboost-stacktrace1.83.0 amd64 1.83.0-3 [280 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libboost-stacktrace1.83-dev amd64 1.83.0-3 [245 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libboost-stacktrace-dev amd64 1.83.0.2+b2 [3592 B] Get: 255 http://deb.debian.org/debian unstable/main amd64 libboost-system-dev amd64 1.83.0.2+b2 [3736 B] Get: 256 http://deb.debian.org/debian unstable/main amd64 libboost-test-dev amd64 1.83.0.2+b2 [3628 B] Get: 257 http://deb.debian.org/debian unstable/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B] Get: 258 http://deb.debian.org/debian unstable/main amd64 libboost-timer1.83.0 amd64 1.83.0-3 [234 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libboost-timer1.83-dev amd64 1.83.0-3 [236 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libboost-timer-dev amd64 1.83.0.2+b2 [3716 B] Get: 261 http://deb.debian.org/debian unstable/main amd64 libboost1.83-tools-dev amd64 1.83.0-3 [1500 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libboost-tools-dev amd64 1.83.0.2+b2 [3768 B] Get: 263 http://deb.debian.org/debian unstable/main amd64 libboost-type-erasure1.83.0 amd64 1.83.0-3 [245 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libboost-type-erasure1.83-dev amd64 1.83.0-3 [248 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libboost-type-erasure-dev amd64 1.83.0.2+b2 [3688 B] Get: 266 http://deb.debian.org/debian unstable/main amd64 libboost-url1.83.0 amd64 1.83.0-3 [336 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libboost-url1.83-dev amd64 1.83.0-3 [422 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 libboost-url-dev amd64 1.83.0.2+b2 [3732 B] Get: 269 http://deb.debian.org/debian unstable/main amd64 libboost-wave1.83.0 amd64 1.83.0-3 [434 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libboost-wave1.83-dev amd64 1.83.0-3 [483 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libboost-wave-dev amd64 1.83.0.2+b2 [3624 B] Get: 272 http://deb.debian.org/debian unstable/main amd64 libboost-all-dev amd64 1.83.0.2+b2 [3936 B] Get: 273 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-1 [249 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libdouble-conversion3 amd64 3.3.0-1+b1 [41.0 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.121-2 [62.7 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.121-2 [22.3 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 libwayland-server0 amd64 1.22.0-2.1+b1 [33.0 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2 [116 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 24.1.2-1 [41.0 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 24.1.2-1 [36.6 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.22.0-2.1+b1 [25.7 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 libxcb-dri2-0 amd64 1.17.0-2 [106 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [107 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2 [105 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2 [108 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [109 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B] Get: 292 http://deb.debian.org/debian unstable/main amd64 libegl-mesa0 amd64 24.1.2-1 [127 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 libegl1 amd64 1.7.0-1+b1 [34.3 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2 [122 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.3.283.0-1 [125 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-10 [34.7 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.1.2-1 [8638 kB] Get: 302 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 24.1.2-1 [151 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB] Get: 304 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 libxau-dev amd64 1:1.0.9-1+b1 [21.3 kB] Get: 308 http://deb.debian.org/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.2-3+b1 [40.8 kB] Get: 309 http://deb.debian.org/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 310 http://deb.debian.org/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-2 [181 kB] Get: 311 http://deb.debian.org/debian unstable/main amd64 libx11-dev amd64 2:1.8.7-1+b1 [875 kB] Get: 312 http://deb.debian.org/debian unstable/main amd64 libglx-dev amd64 1.7.0-1+b1 [15.8 kB] Get: 313 http://deb.debian.org/debian unstable/main amd64 libgl-dev amd64 1.7.0-1+b1 [101 kB] Get: 314 http://deb.debian.org/debian unstable/main amd64 libegl-dev amd64 1.7.0-1+b1 [19.5 kB] Get: 315 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-3 [36.2 kB] Get: 316 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-3 [29.9 kB] Get: 317 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-3 [26.1 kB] Get: 318 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-3 [13.9 kB] Get: 319 http://deb.debian.org/debian unstable/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 320 http://deb.debian.org/debian unstable/main amd64 libevdev2 amd64 1.13.2+dfsg-1 [32.3 kB] Get: 321 http://deb.debian.org/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-1+b2 [779 kB] Get: 322 http://deb.debian.org/debian unstable/main amd64 libfftw3-long3 amd64 3.3.10-1+b2 [344 kB] Get: 323 http://deb.debian.org/debian unstable/main amd64 libfftw3-quad3 amd64 3.3.10-1+b2 [608 kB] Get: 324 http://deb.debian.org/debian unstable/main amd64 libfftw3-single3 amd64 3.3.10-1+b2 [806 kB] Get: 325 http://deb.debian.org/debian unstable/main amd64 libfftw3-bin amd64 3.3.10-1+b2 [52.3 kB] Get: 326 http://deb.debian.org/debian unstable/main amd64 libfftw3-dev amd64 3.3.10-1+b2 [2125 kB] Get: 327 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 328 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.3-1 [1485 kB] Get: 329 http://deb.debian.org/debian unstable/main amd64 libopengl0 amd64 1.7.0-1+b1 [31.1 kB] Get: 330 http://deb.debian.org/debian unstable/main amd64 libglu1-mesa amd64 9.0.2-1.1+b1 [180 kB] Get: 331 http://deb.debian.org/debian unstable/main amd64 libopengl-dev amd64 1.7.0-1+b1 [5380 B] Get: 332 http://deb.debian.org/debian unstable/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1+b1 [219 kB] Get: 333 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 334 http://deb.debian.org/debian unstable/main amd64 libgudev-1.0-0 amd64 238-5 [14.4 kB] Get: 335 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 336 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get: 337 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b1 [35.3 kB] Get: 338 http://deb.debian.org/debian unstable/main amd64 libwacom-common all 2.10.0-2 [62.5 kB] Get: 339 http://deb.debian.org/debian unstable/main amd64 libwacom9 amd64 2.10.0-2 [22.4 kB] Get: 340 http://deb.debian.org/debian unstable/main amd64 libinput-bin amd64 1.26.0-1 [25.1 kB] Get: 341 http://deb.debian.org/debian unstable/main amd64 libmtdev1t64 amd64 1.1.6-1.2 [22.2 kB] Get: 342 http://deb.debian.org/debian unstable/main amd64 libinput10 amd64 1.26.0-1 [130 kB] Get: 343 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 344 http://deb.debian.org/debian unstable/main amd64 libjbig-dev amd64 2.1-6.1+b1 [31.4 kB] Get: 345 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 346 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3 [290 kB] Get: 347 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-3 [71.9 kB] Get: 348 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 349 http://deb.debian.org/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get: 350 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 351 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 352 http://deb.debian.org/debian unstable/main amd64 liblerc-dev amd64 4.0.0+ds-4+b1 [175 kB] Get: 353 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.2-1 [299 kB] Get: 354 http://deb.debian.org/debian unstable/main amd64 libmd4c0 amd64 0.4.8-1+b1 [45.1 kB] Get: 355 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get: 356 http://deb.debian.org/debian unstable/main amd64 libopenmm8.1 amd64 8.1.1+dfsg-1 [1034 kB] Get: 357 http://deb.debian.org/debian unstable/main amd64 libopenmm-dev amd64 8.1.1+dfsg-1 [344 kB] Get: 358 http://deb.debian.org/debian unstable/main amd64 libopenmm-plugins amd64 8.1.1+dfsg-1 [1423 kB] Get: 359 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.42-4+b1 [246 kB] Get: 360 http://deb.debian.org/debian unstable/main amd64 libpng-dev amd64 1.6.43-5 [360 kB] Get: 361 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-6+b1 [245 kB] Get: 362 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5 [758 kB] Get: 363 http://deb.debian.org/debian unstable/main amd64 libqt5core5t64 amd64 5.15.13+dfsg-2 [1837 kB] Get: 364 http://deb.debian.org/debian unstable/main amd64 libqt5concurrent5t64 amd64 5.15.13+dfsg-2 [43.8 kB] Get: 365 http://deb.debian.org/debian unstable/main amd64 libqt5dbus5t64 amd64 5.15.13+dfsg-2 [214 kB] Get: 366 http://deb.debian.org/debian unstable/main amd64 libqt5network5t64 amd64 5.15.13+dfsg-2 [678 kB] Get: 367 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get: 368 http://deb.debian.org/debian unstable/main amd64 libxcb-icccm4 amd64 0.4.1-1.1+b1 [26.8 kB] Get: 369 http://deb.debian.org/debian unstable/main amd64 libxcb-util1 amd64 0.4.0-1+b1 [23.2 kB] Get: 370 http://deb.debian.org/debian unstable/main amd64 libxcb-image0 amd64 0.4.0-2+b1 [22.2 kB] Get: 371 http://deb.debian.org/debian unstable/main amd64 libxcb-keysyms1 amd64 0.4.0-1+b2 [16.4 kB] Get: 372 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get: 373 http://deb.debian.org/debian unstable/main amd64 libxcb-render-util0 amd64 0.3.9-1+b1 [18.3 kB] Get: 374 http://deb.debian.org/debian unstable/main amd64 libxcb-shape0 amd64 1.17.0-2 [105 kB] Get: 375 http://deb.debian.org/debian unstable/main amd64 libxcb-xinerama0 amd64 1.17.0-2 [105 kB] Get: 376 http://deb.debian.org/debian unstable/main amd64 libxcb-xinput0 amd64 1.17.0-2 [130 kB] Get: 377 http://deb.debian.org/debian unstable/main amd64 libxcb-xkb1 amd64 1.17.0-2 [129 kB] Get: 378 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.42-1 [790 kB] Get: 379 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 1.6.0-1+b1 [109 kB] Get: 380 http://deb.debian.org/debian unstable/main amd64 libxkbcommon-x11-0 amd64 1.6.0-1+b1 [16.2 kB] Get: 381 http://deb.debian.org/debian unstable/main amd64 libqt5gui5t64 amd64 5.15.13+dfsg-2 [3450 kB] Get: 382 http://deb.debian.org/debian unstable/main amd64 libqt5widgets5t64 amd64 5.15.13+dfsg-2 [2380 kB] Get: 383 http://deb.debian.org/debian unstable/main amd64 libqt5xml5t64 amd64 5.15.13+dfsg-2 [124 kB] Get: 384 http://deb.debian.org/debian unstable/main amd64 libqt5designer5 amd64 5.15.13-3 [2751 kB] Get: 385 http://deb.debian.org/debian unstable/main amd64 libqt5sql5t64 amd64 5.15.13+dfsg-2 [123 kB] Get: 386 http://deb.debian.org/debian unstable/main amd64 libqt5help5 amd64 5.15.13-3 [150 kB] Get: 387 http://deb.debian.org/debian unstable/main amd64 libqt5opengl5t64 amd64 5.15.13+dfsg-2 [149 kB] Get: 388 http://deb.debian.org/debian unstable/main amd64 libqt5printsupport5t64 amd64 5.15.13+dfsg-2 [204 kB] Get: 389 http://deb.debian.org/debian unstable/main amd64 libqt5test5t64 amd64 5.15.13+dfsg-2 [149 kB] Get: 390 http://deb.debian.org/debian unstable/main amd64 libvulkan-dev amd64 1.3.283.0-1 [1350 kB] Get: 391 http://deb.debian.org/debian unstable/main amd64 libxext-dev amd64 2:1.3.4-1+b1 [107 kB] Get: 392 http://deb.debian.org/debian unstable/main amd64 qt5-qmake-bin amd64 5.15.13+dfsg-2 [1045 kB] Get: 393 http://deb.debian.org/debian unstable/main amd64 qtchooser amd64 66-2 [26.3 kB] Get: 394 http://deb.debian.org/debian unstable/main amd64 qt5-qmake amd64 5.15.13+dfsg-2 [223 kB] Get: 395 http://deb.debian.org/debian unstable/main amd64 qtbase5-dev-tools amd64 5.15.13+dfsg-2 [765 kB] Get: 396 http://deb.debian.org/debian unstable/main amd64 qtbase5-dev amd64 5.15.13+dfsg-2 [1122 kB] Get: 397 http://deb.debian.org/debian unstable/main amd64 libqt5opengl5-dev amd64 5.15.13+dfsg-2 [50.7 kB] Get: 398 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get: 399 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 400 http://deb.debian.org/debian unstable/main amd64 libsharpyuv-dev amd64 1.4.0-0.1 [117 kB] Get: 401 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.0-1 [1096 kB] Get: 402 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-1 [368 kB] Get: 403 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 404 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [110 kB] Get: 405 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1 [123 kB] Get: 406 http://deb.debian.org/debian unstable/main amd64 libwebpdecoder3 amd64 1.4.0-0.1 [204 kB] Get: 407 http://deb.debian.org/debian unstable/main amd64 libwebp-dev amd64 1.4.0-0.1 [442 kB] Get: 408 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 409 http://deb.debian.org/debian unstable/main amd64 libtiffxx6 amd64 4.5.1+git230720-4 [149 kB] Get: 410 http://deb.debian.org/debian unstable/main amd64 libtiff-dev amd64 4.5.1+git230720-4 [462 kB] Get: 411 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1+b1 [232 kB] Get: 412 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.6.3-2 [2744 kB] Get: 413 http://deb.debian.org/debian unstable/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 414 http://deb.debian.org/debian unstable/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get: 415 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b3 [312 kB] Get: 416 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [5465 kB] Get: 417 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.0.7-3 [285 kB] Get: 418 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get: 419 http://deb.debian.org/debian unstable/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get: 420 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 421 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 422 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.12.0-2 [21.0 MB] Get: 423 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get: 424 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 425 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.12.1-1 [3869 kB] Get: 426 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get: 427 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get: 428 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.2.1-1 [1995 kB] Get: 429 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b3 [25.5 kB] Get: 430 http://deb.debian.org/debian unstable/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b1 [299 kB] Get: 431 http://deb.debian.org/debian unstable/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get: 432 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.46.0-1 [1623 kB] Get: 433 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.5-1 [80.7 kB] Get: 434 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 10.3.0-2 [564 kB] Get: 435 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.12.3-3.1 [113 kB] Get: 436 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 10.3.0-2 [79.5 kB] Get: 437 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 438 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 439 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.6.3-2 [8167 kB] Get: 440 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5.sip amd64 12.13.0-1+b1 [79.5 kB] Get: 441 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5 amd64 5.15.10+dfsg-1+b3 [2508 kB] Get: 442 http://deb.debian.org/debian unstable/main amd64 voronota amd64 1.22.3149-2 [2057 kB] Fetched 304 MB in 7s (41.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-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 ... 19685 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.4-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.4-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.4-1_amd64.deb ... Unpacking python3.12-minimal (3.12.4-1) ... Setting up libpython3.12-minimal:amd64 (3.12.4-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.12-minimal (3.12.4-1) ... 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 ... 20005 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.2-1_amd64.deb ... Unpacking python3-minimal (3.12.2-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../6-libpython3.12-stdlib_3.12.4-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.4-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../7-python3.12_3.12.4-1_amd64.deb ... Unpacking python3.12 (3.12.4-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.12.2-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.2-1) ... Setting up python3-minimal (3.12.2-1) ... 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 ... 21007 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.2-1_amd64.deb ... Unpacking python3 (3.12.2-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-4_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-4_amd64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../005-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.22.5-1_amd64.deb ... Unpacking gettext-base (0.22.5-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../008-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.40.1-9_amd64.deb ... Unpacking bsdextrautils (2.40.1-9) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../011-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.12.1-2_amd64.deb ... Unpacking man-db (2.12.1-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../013-libedit2_3.1-20240517-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20240517-1) ... Selecting previously unselected package libcbor0.10:amd64. Preparing to unpack .../014-libcbor0.10_0.10.2-1.2_amd64.deb ... Unpacking libcbor0.10:amd64 (0.10.2-1.2) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../015-libfido2-1_1.15.0-1_amd64.deb ... Unpacking libfido2-1:amd64 (1.15.0-1) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../016-libkrb5support0_1.21.2-1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.2-1) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../017-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../018-libk5crypto3_1.21.2-1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.2-1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../019-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../020-libkrb5-3_1.21.2-1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.2-1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../021-libgssapi-krb5-2_1.21.2-1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.2-1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../022-openssh-client_1%3a9.7p1-6_amd64.deb ... Unpacking openssh-client (1:9.7p1-6) ... Selecting previously unselected package m4. Preparing to unpack .../023-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../024-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../025-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../026-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../027-autopoint_0.22.5-1_all.deb ... Unpacking autopoint (0.22.5-1) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../028-libtcl8.6_8.6.14+dfsg-1_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../029-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../030-libpng16-16t64_1.6.43-5_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.43-5) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../031-libfreetype6_2.13.2+dfsg-1+b4_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... 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Setting up libboost-filesystem1.83.0:amd64 (1.83.0-3) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libboost-url1.83.0:amd64 (1.83.0-3) ... Setting up libpcre2-16-0:amd64 (10.42-4+b1) ... Setting up libopengl0:amd64 (1.7.0-1+b1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libxcb-util1:amd64 (0.4.0-1+b1) ... Setting up libxcb-xkb1:amd64 (1.17.0-2) ... Setting up libxcb-image0:amd64 (0.4.0-2+b1) ... Setting up libkrb5support0:amd64 (1.21.2-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Aug 3 12:30:15 UTC 2025. Universal Time is now: Sun Aug 3 12:30:15 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-3) ... Setting up libxcb-present0:amd64 (1.17.0-2) ... Setting up unicode-data (15.1.0-1) ... Setting up libboost-serialization1.83.0:amd64 (1.83.0-3) ... Setting up xtrans-dev (1.4.0-1) ... Setting up libboost-numpy1.83.0 (1.83.0-3) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libglib2.0-0t64:amd64 (2.80.3-1) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3) ... 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 libxcb-xinerama0:amd64 (1.17.0-2) ... Setting up libpkgconf3:amd64 (1.8.1-3) ... Setting up libmunge2:amd64 (0.5.15-4) ... Setting up libexpat1-dev:amd64 (2.6.2-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up qt5-qmake-bin (5.15.13+dfsg-2) ... Setting up libsqlite3-dev:amd64 (3.46.0-1) ... Setting up libboost-program-options-dev:amd64 (1.83.0.2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-3) ... Setting up libboost-chrono1.83.0t64:amd64 (1.83.0-3) ... Setting up libxcb-sync1:amd64 (1.17.0-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libavahi-common-data:amd64 (0.8-13+b2) ... Setting up libdbus-1-3:amd64 (1.14.10-4+b1) ... Setting up libfftw3-quad3:amd64 (3.3.10-1+b2) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libimagequant0:amd64 (2.18.0-1+b1) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libboost-nowide1.83-dev (1.83.0-3) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libhwloc15:amd64 (2.11.0-1) ... Setting up libboost-stacktrace1.83-dev:amd64 (1.83.0-3) ... Setting up libtcl8.6:amd64 (8.6.14+dfsg-1) ... Setting up autopoint (0.22.5-1) ... Setting up libboost-numpy1.83-dev (1.83.0-3) ... Setting up libjsoncpp25:amd64 (1.9.5-6+b2) ... Setting up icu-devtools (72.1-4+b1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up pkgconf-bin (1.8.1-3) ... Setting up libsensors5:amd64 (1:3.6.0-10) ... Setting up liblerc-dev:amd64 (4.0.0+ds-4+b1) ... Setting up libk5crypto3:amd64 (1.21.2-1) ... Setting up libltdl7:amd64 (2.4.7-7+b1) ... Setting up libfftw3-double3:amd64 (3.3.10-1+b2) ... Setting up libcifpp-data (5.0.7.1-3) ... Setting up libglapi-mesa:amd64 (24.1.2-1) ... Setting up libboost-test1.83.0:amd64 (1.83.0-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:amd64 (14.1.0-2) ... Setting up libboost-fiber1.83.0:amd64 (1.83.0-3) ... Setting up libvulkan1:amd64 (1.3.283.0-1) ... Setting up libboost-atomic1.83-dev:amd64 (1.83.0-3) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.4.0-0.1) ... Setting up liblzma-dev:amd64 (5.6.2-1) ... Setting up libxcb-dri2-0:amd64 (1.17.0-2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libboost-atomic-dev:amd64 (1.83.0.2+b2) ... Setting up libnuma1:amd64 (2.0.18-1) ... Setting up dwz (0.15-1+b1) ... Setting up libmtdev1t64:amd64 (1.1.6-1.2) ... Setting up sensible-utils (0.0.24) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b1) ... Setting up libxshmfence1:amd64 (1.3-1+b1) ... Setting up libboost-exception1.83-dev:amd64 (1.83.0-3) ... Setting up librhash0:amd64 (1.4.3-3+b1) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libxcb-randr0:amd64 (1.17.0-2) ... Setting up libboost-stacktrace-dev:amd64 (1.83.0.2+b2) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-4) ... Setting up libnl-3-200:amd64 (3.7.0-0.3) ... Setting up libboost-graph1.83.0:amd64 (1.83.0-3) ... Setting up libpsm2-2 (11.2.185-2.1) ... Setting up openmpi-common (4.1.6-13.3) ... Setting up clustalw (2.1+lgpl-7) ... Setting up libmd4c0:amd64 (0.4.8-1+b1) ... Setting up libboost-container1.83.0:amd64 (1.83.0-3) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b3) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up netbase (6.4) ... Setting up libboost-type-erasure1.83.0:amd64 (1.83.0-3) ... Setting up cmake-data (3.29.6-1) ... Setting up libkrb5-3:amd64 (1.21.2-1) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up libglu1-mesa:amd64 (9.0.2-1.1+b1) ... Setting up libboost-system1.83-dev:amd64 (1.83.0-3) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... 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 libssh2-1t64:amd64 (1.11.0-5) ... Setting up libboost-math1.83.0:amd64 (1.83.0-3) ... Setting up libopengl-dev:amd64 (1.7.0-1+b1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:amd64 (1.15.0-1) ... Setting up libsharpyuv-dev:amd64 (1.4.0-0.1) ... Setting up libgfortran-13-dev:amd64 (13.3.0-1) ... Setting up python-matplotlib-data (3.6.3-2) ... Setting up libwebpmux3:amd64 (1.4.0-0.1) ... Setting up libtiffxx6:amd64 (4.5.1+git230720-4) ... Setting up libdeflate-dev:amd64 (1.20-1) ... Setting up libopenmm8.1 (8.1.1+dfsg-1) ... Setting up libdrm-common (2.4.121-2) ... Setting up libevdev2:amd64 (1.13.2+dfsg-1) ... Setting up readline-common (8.2-4) ... Setting up libicu-dev:amd64 (72.1-4+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg-3) ... Setting up libboost1.83-tools-dev (1.83.0-3) ... Setting up libgudev-1.0-0:amd64 (238-5) ... Setting up qtchooser (66-2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libwacom-common (2.10.0-2) ... Setting up libxkbcommon0:amd64 (1.6.0-1+b1) ... Setting up libwayland-client0:amd64 (1.22.0-2.1+b1) ... 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 (2024.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up liblapack3:amd64 (3.12.0-3) ... 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 libboost-wave1.83.0:amd64 (1.83.0-3) ... Setting up gettext (0.22.5-1) ... Setting up libboost-coroutine1.83.0:amd64 (1.83.0-3) ... Setting up libxau-dev:amd64 (1:1.0.9-1+b1) ... Setting up libboost-chrono1.83-dev:amd64 (1.83.0-3) ... Setting up qt5-qmake:amd64 (5.15.13+dfsg-2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libboost-math1.83-dev:amd64 (1.83.0-3) ... Setting up libtool (2.4.7-7) ... Setting up libboost-chrono-dev:amd64 (1.83.0.2+b2) ... Setting up libfftw3-bin (3.3.10-1+b2) ... Setting up libwacom9:amd64 (2.10.0-2) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up libboost-log1.83.0 (1.83.0-3) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libboost-math-dev:amd64 (1.83.0.2+b2) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up libboost-system-dev:amd64 (1.83.0.2+b2) ... Setting up libpng-dev:amd64 (1.6.43-5) ... Setting up libavahi-common3:amd64 (0.8-13+b2) ... Setting up libboost-serialization1.83-dev:amd64 (1.83.0-3) ... Setting up libjpeg-dev:amd64 (1:2.1.5-3) ... Setting up libjbig-dev:amd64 (2.1-6.1+b1) ... Setting up libboost-locale1.83.0:amd64 (1.83.0-3) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libboost-test1.83-dev:amd64 (1.83.0-3) ... Setting up libboost-url1.83-dev:amd64 (1.83.0-3) ... Setting up libboost-tools-dev (1.83.0.2+b2) ... Setting up libboost-filesystem1.83-dev:amd64 (1.83.0-3) ... Setting up libboost-exception-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-nowide-dev (1.83.0.2+b2) ... Setting up gfortran-13-x86-64-linux-gnu (13.3.0-1) ... Setting up libopenmm-dev (8.1.1+dfsg-1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-1) ... Setting up pkgconf:amd64 (1.8.1-3) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libinput-bin (1.26.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.18-1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3) ... Setting up libxnvctrl0:amd64 (535.171.04-1) ... Setting up libboost-test-dev:amd64 (1.83.0.2+b2) ... Setting up libcifpp5:amd64 (5.0.7.1-3+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.4.7-7+b1) ... Setting up libxdmcp-dev:amd64 (1:1.1.2-3+b1) ... Setting up libwebp-dev:amd64 (1.4.0-0.1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libboost-timer1.83-dev:amd64 (1.83.0-3) ... Setting up libllvm17t64:amd64 (1:17.0.6-12+b1) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libtiff-dev:amd64 (4.5.1+git230720-4) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ... Setting up libboost-container1.83-dev:amd64 (1.83.0-3) ... Setting up gfortran-13 (13.3.0-1) ... Setting up libboost-date-time1.83-dev:amd64 (1.83.0-3) ... Setting up shared-mime-info (2.4-5) ... Setting up libboost-numpy-dev (1.83.0.2+b2) ... Setting up libxkbcommon-x11-0:amd64 (1.6.0-1+b1) ... Setting up libeigen3-dev (3.4.0-4) ... Setting up libgssapi-krb5-2:amd64 (1.21.2-1) ... Setting up libboost-regex1.83-dev:amd64 (1.83.0-3) ... Setting up pkg-config:amd64 (1.8.1-3) ... Setting up libboost-random1.83-dev:amd64 (1.83.0-3) ... Setting up libboost-serialization-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-date-time-dev:amd64 (1.83.0.2+b2) ... Setting up libjs-sphinxdoc (7.2.6-9) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up libopenmm-plugins (8.1.1+dfsg-1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libdrm2:amd64 (2.4.121-2) ... Setting up libnl-3-dev:amd64 (3.7.0-0.3) ... Setting up groff-base (1.23.0-4) ... Setting up libxslt1.1:amd64 (1.1.35-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libboost-url-dev:amd64 (1.83.0.2+b2) ... Setting up libhwloc-dev:amd64 (2.11.0-1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libboost-regex-dev:amd64 (1.83.0.2+b2) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up libarchive13t64:amd64 (3.7.2-2.1) ... Setting up libfftw3-dev:amd64 (3.3.10-1+b2) ... Setting up libavahi-client3:amd64 (0.8-13+b2) ... Setting up libboost-timer-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-filesystem-dev:amd64 (1.83.0.2+b2) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Setting up libdrm-amdgpu1:amd64 (2.4.121-2) ... Setting up libboost-thread1.83-dev:amd64 (1.83.0-3) ... Setting up libinput10:amd64 (1.26.0-1) ... Setting up libibverbs1:amd64 (52.0-2) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libboost-json1.83-dev:amd64 (1.83.0-3) ... Setting up libxcb1-dev:amd64 (1.17.0-2) ... Setting up libboost-wave1.83-dev:amd64 (1.83.0-3) ... Setting up libpython3.12-stdlib:amd64 (3.12.4-1) ... Setting up libboost-locale1.83-dev:amd64 (1.83.0-3) ... Setting up libcurl4t64:amd64 (8.8.0-1) ... Setting up libgbm1:amd64 (24.1.2-1) ... Setting up ibverbs-providers:amd64 (52.0-2) ... Setting up libdrm-radeon1:amd64 (2.4.121-2) ... Setting up libboost-iostreams1.83-dev:amd64 (1.83.0-3) ... Setting up openssh-client (1:9.7p1-6) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up python3.12 (3.12.4-1) ... Setting up libdrm-intel1:amd64 (2.4.121-2) ... Setting up libgl1-mesa-dri:amd64 (24.1.2-1) ... Setting up libboost-type-erasure1.83-dev:amd64 (1.83.0-3) ... Setting up libx11-dev:amd64 (2:1.8.7-1+b1) ... Setting up libboost-random-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-locale-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-wave-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-iostreams-dev:amd64 (1.83.0.2+b2) ... Setting up dssp (4.2.2-2) ... Setting up libhwloc-plugins:amd64 (2.11.0-1) ... Setting up man-db (2.12.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-graph1.83-dev:amd64 (1.83.0-3) ... Setting up libboost-container-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-type-erasure-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-context1.83-dev:amd64 (1.83.0-3) ... Setting up libpython3.12t64:amd64 (3.12.4-1) ... Setting up libnl-route-3-dev:amd64 (3.7.0-0.3) ... Setting up libboost-coroutine1.83-dev:amd64 (1.83.0-3) ... Setting up libqt5core5t64:amd64 (5.15.13+dfsg-2) ... Setting up libegl-mesa0:amd64 (24.1.2-1) ... Setting up libboost-fiber1.83-dev:amd64 (1.83.0-3) ... Setting up libraqm0:amd64 (0.10.1-1+b1) ... Setting up libevent-dev (2.1.12-stable-10) ... Setting up libpmix2t64:amd64 (5.0.2-3) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b1) ... Setting up libegl1:amd64 (1.7.0-1+b1) ... Setting up libqt5sql5t64:amd64 (5.15.13+dfsg-2) ... Setting up cmake (3.29.6-1) ... Setting up librdmacm1t64:amd64 (52.0-2) ... Setting up libboost-coroutine-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-log1.83-dev (1.83.0-3) ... Setting up libboost-json-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-log-dev (1.83.0.2+b2) ... Setting up libcups2t64:amd64 (2.4.10-1) ... Setting up libpmix-dev:amd64 (5.0.2-3) ... Setting up libhsakmt1:amd64 (5.7.0-1) ... Setting up libboost-thread-dev:amd64 (1.83.0.2+b2) ... Setting up libpython3-stdlib:amd64 (3.12.2-1) ... Setting up libboost-fiber-dev:amd64 (1.83.0.2+b2) ... Setting up libfabric1:amd64 (1.17.0-3+b1) ... Setting up libboost-graph-dev:amd64 (1.83.0.2+b2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libqt5dbus5t64:amd64 (5.15.13+dfsg-2) ... Setting up libglx-mesa0:amd64 (24.1.2-1) ... Setting up libglx0:amd64 (1.7.0-1+b1) ... Setting up libqt5concurrent5t64:amd64 (5.15.13+dfsg-2) ... Setting up blt (2.5.3+dfsg-7) ... Setting up libqt5network5t64:amd64 (5.15.13+dfsg-2) ... Setting up libqt5xml5t64:amd64 (5.15.13+dfsg-2) ... Setting up debhelper (13.16) ... Setting up python3 (3.12.2-1) ... Setting up libpython3.12-dev:amd64 (3.12.4-1) ... Setting up libboost-context-dev:amd64 (1.83.0.2+b2) ... Setting up libqt5test5t64:amd64 (5.15.13+dfsg-2) ... Setting up libibverbs-dev:amd64 (52.0-2) ... Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-pil:amd64 (10.3.0-2) ... Setting up qtbase5-dev-tools (5.15.13+dfsg-2) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.0-1) ... Setting up libgl1:amd64 (1.7.0-1+b1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-brotli (1.1.0-2+b3) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.5-1) ... Setting up python3.12-dev (3.12.4-1) ... Setting up python3-pyqt5.sip (12.13.0-1+b1) ... Setting up python3-lxml:amd64 (5.2.1-1) ... Setting up libhsa-runtime64-1 (5.7.1-2) ... Setting up libglx-dev:amd64 (1.7.0-1+b1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-lib2to3 (3.12.3-3.1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up libgl-dev:amd64 (1.7.0-1+b1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-3.1) ... python3.12: can't get files for byte-compilation Setting up python3-sympy (1.12.1-1) ... Setting up python3-attr (23.2.0-2) ... Setting up libvulkan-dev:amd64 (1.3.283.0-1) ... Setting up libpython3-dev:amd64 (3.12.2-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up libegl-dev:amd64 (1.7.0-1+b1) ... Setting up python3-lz4 (4.0.2+dfsg-1+b3) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b1) ... Setting up python3-tk:amd64 (3.12.3-3.1) ... Setting up python3-fs (2.4.16-4) ... Setting up libqt5gui5t64:amd64 (5.15.13+dfsg-2) ... Setting up libamdhip64-5 (5.7.1-3) ... Setting up python3-pil.imagetk:amd64 (10.3.0-2) ... Setting up python3-dev (3.12.2-1) ... Setting up libboost-python1.83-dev (1.83.0-3) ... Setting up libglu1-mesa-dev:amd64 (9.0.2-1.1+b1) ... Setting up python3-numpy (1:1.26.4+ds-10) ... Setting up python3-contourpy (1.0.7-3) ... Setting up dh-python (6.20240422) ... Setting up libucx0:amd64 (1.17.0+ds-1) ... Setting up python3-scipy (1.12.0-2) ... Setting up libqt5widgets5t64:amd64 (5.15.13+dfsg-2) ... Setting up libqt5help5:amd64 (5.15.13-3) ... Setting up libboost-python-dev (1.83.0.2+b2) ... Setting up libopenmpi3t64:amd64 (4.1.6-13.3) ... Setting up libqt5opengl5t64:amd64 (5.15.13+dfsg-2) ... Setting up libboost-mpi1.83.0 (1.83.0-3) ... Setting up openmpi-bin (4.1.6-13.3) ... 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 libqt5printsupport5t64:amd64 (5.15.13+dfsg-2) ... Setting up libboost-graph-parallel1.83.0 (1.83.0-3) ... Setting up libqt5designer5:amd64 (5.15.13-3) ... Setting up mpi-default-bin (1.15) ... Setting up qtbase5-dev:amd64 (5.15.13+dfsg-2) ... Setting up libopenmpi-dev:amd64 (4.1.6-13.3) ... 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 libboost-graph-parallel1.83-dev (1.83.0-3) ... Setting up python3-pyqt5 (5.15.10+dfsg-1+b3) ... Setting up libboost-mpi-python1.83.0 (1.83.0-3) ... Setting up libqt5opengl5-dev:amd64 (5.15.13+dfsg-2) ... Setting up libboost-graph-parallel-dev (1.83.0.2+b2) ... Setting up mpi-default-dev (1.15) ... Setting up libboost-mpi1.83-dev (1.83.0-3) ... Setting up libboost-mpi-dev (1.83.0.2+b2) ... Setting up libboost-mpi-python1.83-dev (1.83.0-3) ... Setting up libboost-mpi-python-dev (1.83.0.2+b2) ... Setting up libboost-all-dev (1.83.0.2+b2) ... Setting up python3-fonttools (4.46.0-1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-2) ... Processing triggers for libc-bin (2.38-13) ... 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 I: Building the package I: Running cd /build/reproducible-path/openstructure-2.6.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../openstructure_2.6.1-1~exp_source.changes dpkg-buildpackage: info: source package openstructure dpkg-buildpackage: info: source version 2.6.1-1~exp dpkg-buildpackage: info: source distribution experimental 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/reproducible-path/openstructure-2.6.1' 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 && DEB_PYTHON_INSTALL_LAYOUT=deb 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 13.3.0 -- The C compiler identification is GNU 13.3.0 -- 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 CMake Warning (dev) at cmake_support/OST.cmake:892 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): cmake_support/OST.cmake:921 (get_compiler_version) CMakeLists.txt:174 (setup_compiler_flags) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Python: /usr/bin/python3 (found suitable version "3.12.4", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- Found Boost package: python312 -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: unit_test_framework -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: filesystem system -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: iostreams -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: program_options -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: regex -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: thread -- 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 "1.3.1") -- Found PNG: /usr/lib/x86_64-linux-gnu/libpng.so (found version "1.6.43") -- Found FFTW: /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Found TIFF: /usr/lib/x86_64-linux-gnu/libtiff.so (found version "4.5.1") -- 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 (4.9s) -- Generating done (1.0s) 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/openstructure-2.6.1' dh_auto_build cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/openstructure-2.6.1 -B/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/openstructure-2.6.1/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 -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/base/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/create_stage.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 -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/subst___init__.py.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod/CMakeFiles/ost_bindings_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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/conop/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/pymod/CMakeFiles/ost_conop_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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/db/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/pymod/CMakeFiles/ost_db_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/pymod /build/reproducible-path/openstructure-2.6.1/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 -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/gfx/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/gui/share /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share/CMakeFiles/scene_icons.dir/DependInfo.cmake "--color=" make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/gui/share /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share /build/reproducible-path/openstructure-2.6.1/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 -f modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/depend make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.6.1/modules/base/pymod/__init__.py.in -DOUT_FILE=__init__.py -DALL_ADDITIONAL_MODULES=,\'gui\',\'gfx\',\'img\',\'info\' -P /build/reproducible-path/openstructure-2.6.1/cmake_support/substitute.cmake make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib 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 make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/depend make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/info/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/ost_info_pymod.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/depend 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/io/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/pymod/CMakeFiles/ost_io_pymod.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]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build.make modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/images/logo-small.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/images/logo-small.png make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/conop/pymod/./__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/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 make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/db/pymod/./__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/db/./__init__.py make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/./__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/geom/./__init__.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/pymod/./__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gfx/./__init__.py 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/add_icon.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/add_icon.png 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/__init__.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/dng/__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build make -f modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build.make modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/./__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./__init__.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/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/./__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/img/./__init__.py make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/seq/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/scripts /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_startup.py.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/scripts /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_config.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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/img/alg/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/close_icon.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/close_icon.png cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/color_options_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/color_options_widget.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/pymod/./__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/info/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/pymod/./py_gfx_obj.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gfx/./py_gfx_obj.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/./__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/bin cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/pymod/./__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/mm/./__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 make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/conop/pymod/./cleanup.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/conop/./cleanup.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./__init__.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./lga.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./lga.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/./init_context_menu.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_context_menu.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/pymod/./__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/io/./__init__.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/dng/termuse.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/termuse.py [ 0%] Built target subst___init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' 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]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/pymod/./__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/./__init__.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/alg/./__init__.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/pymod/./antechamber.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/mm/./antechamber.py [ 0%] Built target ost_db_pymod make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/depend cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/critical_icon.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/critical_icon.png make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/scripts /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/actions /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/actions /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/color_select_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/color_select_widget.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/scripts /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./views.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./views.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./hbplus.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hbplus.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.6.1/scripts/ost_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.12.4 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/dist-packages/ -P /build/reproducible-path/openstructure-2.6.1/cmake_support/substitute.cmake make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 0%] Built target gui_images cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/pymod/./mat.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/alg/./mat.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/pymod/./remote.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/io/./remote.py [ 0%] Built target ost_img_pymod make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 0%] Built target ost_geom_pymod make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/combo_options_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/combo_options_widget.py make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./superpose.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./superpose.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.6.1/scripts/ost_config.in -DOUT_FILE=ost_config -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.12.4 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/dist-packages/ -P /build/reproducible-path/openstructure-2.6.1/cmake_support/substitute.cmake cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/./init_menubar.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_menubar.py [ 0%] Built target ost_gfx_pymod make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/build cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/delete_icon.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/delete_icon.png make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/depend cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/dng/superpositiondialog.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/superpositiondialog.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.6.1/scripts/ost.in -DOUT_FILE=ost -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.12.4 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/dist-packages/ -P /build/reproducible-path/openstructure-2.6.1/cmake_support/substitute.cmake make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/actions/ost-compare-ligand-structures /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-ligand-structures cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./msms.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./msms.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 0%] Built target ost_img_alg_pymod [ 0%] Built target ost_seq_pymod [ 0%] Built target ost_mol_pymod cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/ost_base_pymod.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 0%] Built target ost_conop_pymod make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.6.1/scripts/dng.in -DOUT_FILE=dng -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.12.4 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/dist-packages/ -P /build/reproducible-path/openstructure-2.6.1/cmake_support/substitute.cmake cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/pymod/./repository.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/io/./repository.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/tests cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/pymod/./renumber.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/alg/./renumber.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/./init_spacenav.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_spacenav.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/cpk_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/cpk_widget.py [ 0%] Built target ost_info_pymod cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./qsscoring.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./qsscoring.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 0%] Built target ost_mol_mm_pymod cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./tmtools.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./tmtools.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/distance_icon.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/distance_icon.png make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/build cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/dng/init.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/init.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/pymod/./settings.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./settings.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/./init_splash.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_splash.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/custom_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/custom_widget.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./trajectory_analysis.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./trajectory_analysis.py [ 0%] Built target subst_ost_startup.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/pymod/./aaindex.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/alg/./aaindex.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/pymod/./stutil.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./stutil.py [ 0%] Built target subst_ost_config cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/actions/ost-compare-structures /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-structures cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/dng/menu.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/menu.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/find_icon.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/find_icon.png [ 0%] Built target subst_dng cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/gradient_editor_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_editor_widget.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./dssp.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./dssp.py [ 0%] Built target ost_io_pymod [ 0%] Built target subst_ost cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./structure_analysis.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./structure_analysis.py [ 0%] Built target create_stage cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/./trajectory_viewer.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./trajectory_viewer.py make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/depend cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/pymod/aaindex1 /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex1 cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/actions/ost-compare-structures-legacy /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-structures-legacy cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/pymod/./table.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./table.py make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/geom/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom_headers.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/gradient_info_handler.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_info_handler.py make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend 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]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/config /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/config /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config_headers.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./clustalw.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./clustalw.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/base/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/ost_base_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/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/depend cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src /build/reproducible-path/openstructure-2.6.1/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/depend make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/information_icon.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/information_icon.png make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/depend cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/info/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src/CMakeFiles/ost_info_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 make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/bindings/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/conop/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/db/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/src/CMakeFiles/ost_db_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/depend make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/DependInfo.cmake "--color=" 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[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/img/base/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_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 make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./utils.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./utils.py 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 cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/./helpwidget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./helpwidget.py make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./helix_kinks.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./helix_kinks.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/pymod/aaindex2 /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex2 make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/io/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src/CMakeFiles/ost_io_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/pymod/./table_selector.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./table_selector.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/gradient_list_model.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_list_model.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/gfx/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/export_helper/generic_property_def.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/generic_property_def.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/gui/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/export_helper/vector.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/export_helper/vector.hh make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/config/./base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./base.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 make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/pointer_iterator.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/conop/src/./conop.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./conop.hh 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/map_icon.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/map_icon.png make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/DependInfo.cmake "--color=" make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build [ 0%] Built target actions make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./info.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/gradient_preset_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_preset_widget.py 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 cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/pymod/./xmlrunner.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./xmlrunner.py 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/./wrap_tmalign.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/bindings/./wrap_tmalign.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 0%] Built target ost_gui_dng_pymod make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./anisotropic.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./anisotropic.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./alignment_opts.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./alignment_opts.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_iso_gen.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/export_helper/pair_to_tuple_conv.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./naccess.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./naccess.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/./table.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./table.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./hbond.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./hbond.py make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/pymod/aaindex3 /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex3 cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/impl/sequence_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./def.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./def.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/atom_group.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_group.hh make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/build cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/hsc_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/hsc_widget.py 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 make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/raster_image/raster_image.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./svd_superpose.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./svd_superpose.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/chemdict_parser.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/menubar_icon.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/menubar_icon.png cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./forcefield.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./forcefield.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/conop/src/./processor.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./processor.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./auto_correlate.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./info_error.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_error.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/./gosty_startup.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./gosty_startup.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./hhblits.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hhblits.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/pymod/./testutils.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./testutils.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./clip_alignment.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/star_parser.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/star_parser.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./module_config.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/export_helper/vec_to_list_conv.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/export_helper/vec_to_list_conv.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./lddt.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./lddt.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/impl/sequence_impl_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/immutable_gradient_info_handler.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/immutable_gradient_info_handler.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/atom_prop.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./exc.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./exc.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/config/./config.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./config.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/rigid_body_manipulator_icon.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/rigid_body_manipulator_icon.png cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_option_group.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/dispatch.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/dispatch.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./clear.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clear.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./info_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./hhblits2.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hhblits2.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./ff_reader.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./ff_reader.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/immutable_preset_info_handler.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/immutable_preset_info_handler.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/db/src/./sqlite_wrap.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different __init__.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/__init__.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./sec_structure_segments.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/mmcif_reader.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh [ 0%] Built target ost_bindings_headers cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/atom_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/impl/sequence_list_impl_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh [ 0%] Built target ost_seq_alg_pymod cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./qsscore.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./qsscore.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/conop/src/./amino_acids.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./amino_acids.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/test_utils/compare_files.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/test_utils/compare_files.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_options.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/config/./dllexport.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./dllexport.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./geom.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./geom.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/selection_icon.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/selection_icon.png cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./hhblits3.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hhblits3.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_iso_spec.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./conservation.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./conservation.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./info_impl_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/db/src/./sqlite_conv.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_conv.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/atom_impl_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./buildingblock.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./buildingblock.hh [ 0%] Built target ost_gui_pymod cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./clip_min_max.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/impl/sequence_list_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/mmcif_info.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/init_inspector.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/init_inspector.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./local_dist_diff_test.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./local_dist_diff_test.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./generic_property.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./generic_property.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_bar.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./scoring.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./scoring.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/conop/src/./diag.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./diag.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./blast.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./blast.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/impl/sequence_list_iterator.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/io_profile.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./contact_prediction_score.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/config/./version.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./version.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./info_handle.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_handle.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./mat.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/chain_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/show_sidebar_icon.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/show_sidebar_icon.png cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_octree.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./conjugate.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./conjugate.hh [ 0%] Built target ost_base_pymod cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/db/src/./module_config.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/db/./module_config.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./integrity_error.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./integrity_error.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/./sequence_list.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_list.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./block_modifiers.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./block_modifiers.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/dcd_io.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/inspector_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/inspector_widget.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./chain_mapping.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./chain_mapping.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./contact_weight_matrix.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/selection_tool.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/conop/src/./model_check.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./model_check.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/db/src/./linear_indexer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/db/./linear_indexer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/chain_impl_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/octree_isocont.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./mat2.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat2.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./distance_test_common.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./invalid_handle.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./invalid_handle.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/site_icon.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/site_icon.png cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./info_group.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_group.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./cadscore.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./cadscore.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/map_level_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/map_level_widget.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/./sequence_handle.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_handle.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/conop/src/./heuristic.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./heuristic.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./convolute.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./convolute.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./gromacs_block_modifiers.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./gromacs_block_modifiers.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./ptr_observer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./ptr_observer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/measure_tool.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./distance_map.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/db/src/./binary_container.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/db/./binary_container.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/split_icon.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/split_icon.png cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./stereochemistry.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./stereochemistry.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/connector_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_crd_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./mat3.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat3.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./distance_rmsd_test.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_rmsd_test.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/cartoon_renderer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./kclust.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./kclust.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/./alignment_handle.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./alignment_handle.hh [ 0%] Built target ost_config_headers make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/config /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/config /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/preset.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_option.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./info_item.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_item.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./correlate.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./correlate.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/conop/src/./compound.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/db/src/./extract_data_helper.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/db/./extract_data_helper.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/warning_icon.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/warning_icon.png cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./ligand_scoring.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./ligand_scoring.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./heuristic_block_modifiers.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./heuristic_block_modifiers.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./ialign.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./ialign.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/custom_renderer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/connector_impl_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./mat4.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat4.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./entropy.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./entropy.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/./module_config.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./module_config.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./superpose_frames.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_base_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base_fw.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./log.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./log.hh make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_pqr_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pqr_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_manager.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/remote.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/remote.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./dockq.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./dockq.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'modules/config/CMakeFiles/ost_config.dir/build'. make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/share/icons/refresh.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/refresh.png make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./vec.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./cross_correlate.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./cross_correlate.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./interaction.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./interaction.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./mmseqs2.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./mmseqs2.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./info_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/conop/src/./compound_lib.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./filter_clashes.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_mae_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mae_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/cpk_renderer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/./contact_score.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./contact_score.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_options_widget.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_def.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./global_align.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./global_align.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 0%] Built target ost_db_headers cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/./sequence_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_op.hh [ 0%] Built target ost_config cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/dihedral.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/dihedral.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./log_sink.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./log_sink.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/preset_editor_list_model.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_editor_list_model.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./vec2.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec2.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./settings.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./settings.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_mmcif_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/conop/src/./module_config.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./module_config.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./module_config.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./module_config.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./density_slice.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./density_slice.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/./dockq.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./dockq.py [ 0%] Built target scene_icons cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./construct_cbeta.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./ins_del.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/./aligned_region.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_region.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_factory.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_factory.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/debug_renderer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/pymod/stereo_data.json /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/stereo_data.json cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/preset_editor_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_editor_widget.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/manipulator.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/manipulator.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./vec3.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec3.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./profile.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./profile.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/conop/src/./rule_based.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./rule_based.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./dft.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./dft.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./simulation.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./simulation.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_frequency_domain.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./info_path.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_path.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./clash_score.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./local_align.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./local_align.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/preset_info_handler.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_info_handler.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/./aligned_column.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_options_win.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_reader.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./dyn_cast.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./dyn_cast.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/simple_renderer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/conop/src/./minimal_compound_lib.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./trajectory_analysis.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./vec4.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec4.hh [ 0%] Built target ost_bindings_pymod cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./modeller.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./modeller.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/preset_list_model.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_list_model.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./fft.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fft.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./merge_pairwise_alignments.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./info_set.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_set.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./stdint.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./stdint.hh [ 0%] Built target ost_mol_alg_pymod cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/sline_renderer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/./aligned_column_iterator.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/mouse_event.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_pdb_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pdb_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./fftw_helper.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fftw_helper.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./vecmat_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/conop/src/./compound_lib_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./observer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./observer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./stdint_msc.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./stdint_msc.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./structure_analysis.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/fragment_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/preset_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_widget.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/map_tool.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/map_tool.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./module_config.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./info_visitor.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_visitor.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./fill.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fill.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./vecmat2_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_writer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/trace_renderer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_spatial_domain.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/./invalid_sequence.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./range.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./range.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./pair_subst_weight_matrix.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/conop/src/./ring_finder.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/./ring_finder.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/align_properties_painter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/render_mode_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/render_mode_widget.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/fragment_impl_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_sdf_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./info_verbose_visitor.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./consistency_checks.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./state_extractor.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./state_extractor.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_visitor.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./filter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./filter.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./vecmat3_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/line_trace_renderer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/sdf_reader.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_reader.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/render_op.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/render_op.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./semiglobal_align.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/query_ast.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/./views_from_sequences.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./module_config.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./module_config.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./pdbize.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/base_row.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_row.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./system_creator.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./system_creator.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./item_type.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type.hh [ 0%] Built target ost_conop_headers cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/sdf_writer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/render_options_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/render_options_widget.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/backbone_trace.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_algorithm.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./vecmat4_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./adjacency_bitmap.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./fourier_filters.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./units.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./units.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/./profile_handle.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/./profile_handle.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./sequence_identity.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_identity.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./topology_creator.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology_creator.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/query_ast_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/save_entity.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/save_entity.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/background_painter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./geom_info_conversion.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/scene_observer_impl.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/scene_observer_impl.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./consistency_checks.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./gaussian_gradient_magnitude.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./circular_iterator.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./circular_iterator.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/query_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/entity_detail.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./sequence_similarity.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/info/src/./item_type_cast.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type_cast.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/conservation_painter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./index.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./index.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/load_entity.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_entity.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./message.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./message.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_visitor_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./gaussian.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/entity_renderer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/scene_selection_helper.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/scene_selection_helper.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/painter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/painter.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./contact_overlap.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./constants.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./constants.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/surface_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/query_impl_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/index.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/index.hh [ 0%] Built target ost_seq_headers cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./platform.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./platform.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./subst_weight_matrix.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./topology.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/simple_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/simple_widget.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/secstr_row.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/secstr_row.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./domain_find.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./gaussian_laplacian.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/trace_renderer_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./composite.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite.hh [ 0%] Built target ost_info_headers cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/residue_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/type_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/type_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/load_surface.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_surface.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/./steep.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./steep.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./similarity_matrix.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./string_ref.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./string_ref.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/sline_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/sline_widget.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./highest_peak_search_3d.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./variance_map.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./composite2.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/seq_secstr_painter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_secstr_painter.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/surface_io_msms_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./accessibility.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./accessibility.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/value_holder.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/value_holder.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/residue_impl_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./histogram.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./histogram.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/connect_renderer_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./pod_vector.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./pod_vector.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./sec_struct.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_struct.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/toolbar_options_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/toolbar_options_widget.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./line_iterator.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./algorithm.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./algorithm.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_str.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./composite3.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./local_sigma_threshold.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/seq_selection_painter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_selection_painter.hh [ 0%] Built target ost_mol_mm_headers cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/mapped_property.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/sdf_str.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_str.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/trace_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/trace_widget.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./fixed_string.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./fixed_string.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./nonstandard.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./nonstandard.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/surface_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./mask_image.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./mask_image.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./composite_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./circle_mask.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./circle_mask.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/seq_text_painter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_text_painter.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/mmcif_str.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_str.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./molck.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./molck.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/tube_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/tube_widget.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./tri_matrix.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./tri_matrix.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/entity_renderer_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./composite_mask.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./composite_mask.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/uniform_color_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/uniform_color_widget.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./find_membrane.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/surface_impl_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./negate.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./negate.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_delegate.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./hmm_pseudo_counts.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./entity_to_density.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/stereochemical_params_reader.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./composite2_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/visibility_op.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/visibility_op.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./boost_filesystem_helper.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/tabulated_trig.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./normalizer_factory.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./data_algorithm.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_algorithm.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/torsion_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/./biounit.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./biounit.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_model.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_model.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/line_trace_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/line_trace_widget.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/base/src/./paged_array.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/./paged_array.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./composite3_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/./hmm_score.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_row.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_row.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./data_observer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_observer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/fast_spheres.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/omf.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./norm.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/torsion_impl_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh [ 0%] Built target ost_mol_alg_headers cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./aligned_cuboid.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./data_types.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data_types.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/wireframe_widget.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/wireframe_widget.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./atom_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./normalizer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/load_map.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/load_map.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./vec_mat_predicates.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/render_options.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh [ 0%] Built target ost_base_headers [ 0%] Built target ost_seq_alg_headers cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_table_view.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_table_view.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/pymod/scene/query_editor.py /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/query_editor.py cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./atom_handle.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_handle.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./norm_linear.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./quat.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./quat.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_df3_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./data.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./data.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_viewer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/line_render_options.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./transform.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./transform.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./atom_view.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_view.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./norm_log.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_log.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/tick_painter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/tick_painter.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/image_format.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/image_format.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/custom_render_options.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/custom_render_options.hh [ 0%] Built target ost_gui_scene_pymod cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./point_cloud.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./point_cloud.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./debug.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./debug.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./bond_handle.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_handle.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/title_row.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/title_row.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/cpk_render_options.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_dx_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./dllexport.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./dllexport.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./norm_od.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_od.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/geom/src/./module_config.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/./module_config.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./bond_table.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_table.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/alignment_view_object.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/alignment_view_object.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./extent_iterator.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_iterator.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/simple_render_options.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_spi_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./power_spectrum.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./chain_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/base_view_object.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_view_object.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./extent_mask.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_mask.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./chain_handle.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_handle.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/sline_render_options.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./chain_view.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_view.hh [ 0%] Built target ost_geom_headers cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_view_object.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_view_object.hh make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/depend cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_situs_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/line_trace_render_options.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/geom/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./extent.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./extent.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./randomize.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./randomize.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./chain_type.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_type.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./image_factory.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_factory.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./smooth_mask_image.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./chem_class.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_class.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/main_thread_runner.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/main_thread_runner.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./image_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_fw.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat4.cc.o [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat3.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/src/mat4.cc [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vec3.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/src/mat3.cc [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat2_op.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/src/vec3.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./stat.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/cartoon_render_options.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/src/vecmat2_op.cc [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/src/vecmat4_op.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/src/transform.cc [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2_op.cc.o [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat2.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/output_redirector.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/quat.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/src/mat2.cc [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat3_op.cc.o [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/src/quat.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/src/composite2_op.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/src/composite2.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/src/vecmat3_op.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/src/composite3.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/src/aligned_cuboid.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./chem_type.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_type.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/src/point_cloud.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_mrc_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3_op.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./stat_accumulator.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/src/composite3_op.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/completer_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/completer_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./image_handle_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./coord_group.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_group.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/trace_render_options.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./image_handle.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/dir_model.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./coord_source.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_source.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_dat_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./stat_min_max.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/color_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./threshold.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./threshold.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_ipl_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./in_mem_coord_source.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./in_mem_coord_source.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/by_element_color_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/gutter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./coord_frame.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_frame.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./image_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_impl.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./transcendentals.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/path_completer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/by_chain_color_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_jpk_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./image_list.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_list.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./transform.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./editor_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_context_parser.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/uniform_color_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_nanoscope_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./image_state_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./transform_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./editor_type_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/gradient_color_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_completer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./image_state.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_png_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./mol.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./mol.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./alg_transform.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_transform.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/entity_view_color_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_dm3_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_shell.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_tiff_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./image.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./image.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./inverted_mask.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./inverted_mask.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/basic_gradient_color_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./alg_mirror.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_mirror.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./entity_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_shell_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/tiff_util.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/tiff_util.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./map.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./map.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/gradient_level_color_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./alg_shift.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./entity_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_shell_widget.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/jpk_util.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/jpk_util.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./mask_base_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./discrete_shrink.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./mask_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./entity_handle.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_handle.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_tokenizer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_tokenizer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/sequence_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/map_handle_color_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./mask_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./entity_observer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./transformation_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./mask_visitor.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_visitor.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_syntax_highlighter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/fasta_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./entity_observer_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./render_pass.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_pass.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/pir_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./transformations.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformations.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/text_logger.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./mask.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./entity_property_mapper.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./bitmap_io.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./module_config.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./module_config.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_interpreter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./fractional_shift.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fractional_shift.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/promod_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./collada_exporter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./color.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./color.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./entity_view.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_view.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_interpreter_worker.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./module_config.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./entity_visitor.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/profile_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./normalizer_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./entity.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./entity_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_shell_text_document_layout.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./polar.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./polar.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/hhm_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/hhm_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./gl_helper.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_helper.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./normalizer_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_impl.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./entity_visitor_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./gfx.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/shell_history.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./line_average.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_average.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/pssm_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pssm_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./null_data.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./null_data.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./gfx_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./handle_type_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./observable.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./observable.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./gfx_node.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/clustal_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/state_machine.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./ics_editor.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./ics_editor.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/./rscrosscorr.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./rscrosscorr.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./paste_impl.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./paste_impl.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./gfx_node_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./peak.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./peak.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/state.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./not_connected_error.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./not_connected_error.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./phase.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./phase.hh [ 1%] Built target ost_img_alg_headers cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/load.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/load.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./gfx_node_visitor.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./property_id.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./property_id.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./physical_units.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./physical_units.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./pixel_sampling.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./pixel_sampling.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./query.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/transition.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/save.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/save.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./gfx_object_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/transition_guard.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./binary_data_sink.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_sink.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./query_error.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_error.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./point_list.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./point_list.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./gfx_object.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/button_bar.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_bar.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./query_state.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_state.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./io_manager.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_manager.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./point.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./point.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/drop_box.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/drop_box.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./gfx_object_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./residue_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/panel_bar.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./polygon_mask.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./polygon_mask.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./binary_data_source.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_source.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./residue_handle.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_handle.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./progress.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./progress.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./gfx_prim.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./module_config.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./module_config.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/panel_manager.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_manager.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./residue_prop.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_prop.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./symmetry_node.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./size.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./size.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/bottom_bar.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/bottom_bar.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./container_serialization.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./container_serialization.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./gfx_test_object.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./residue_view.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_view.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./glwin_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glwin_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./spherical_mask.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./spherical_mask.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/button_box.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_box.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./input.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./input.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./swap_util.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./swap_util.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./sec_structure.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./sec_structure.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/event_button.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/event_button.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./io_utils.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_utils.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./util.cc /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./util.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/panel_widget_container.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_widget_container.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./prim_list.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./prim_list.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./spatial_organizer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./util.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./util.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./io_exception.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_exception.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/panel_bar_widget_holder.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar_widget_holder.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./scene.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./value_util.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./value_util.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./surface.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./convert.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./convert.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./selection.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./selection.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/side_bar.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/side_bar.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./surface_builder.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_builder.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./surface.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./surface.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./vecmat.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./vecmat.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./converting_streams.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./converting_streams.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/splitter_panel_bar.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/splitter_panel_bar.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./texture.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./texture.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./builder.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./builder.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/./mask_info_convert.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_info_convert.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./formatted_line.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./formatted_line.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/tabbed_panel_bar.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/tabbed_panel_bar.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./vertex_array.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./surface_handle.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_handle.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/chemdict_parser.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./chemdict_parser.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/star_parser.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./star_parser.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./surface_prop.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_prop.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/context_menu.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/context_menu.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./vertex_array_helper.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh [ 1%] Built target ost_img_headers cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./torsion_handle.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./torsion_handle.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/mmcif_reader.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_reader.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./scene_observer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene_observer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./transfer_connectivity.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./transfer_connectivity.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/current_selection_node.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/current_selection_node.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/mmcif_info.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_info.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./gl_include.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_include.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./query_view_wrapper.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_view_wrapper.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/io_profile.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./io_profile.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/custom_part_node.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/custom_part_node.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./glext_include.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glext_include.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./view_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/dcd_io.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./dcd_io.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/entity_node.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_node.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./view_type_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_type_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./render_mode.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_mode.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/entity_part_node.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_part_node.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/entity_io_crd_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./material.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./material.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./view_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/gfx_scene_node.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/gfx_scene_node.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/entity_io_pqr_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./gradient.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/label_node.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/label_node.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./xcs_editor.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./xcs_editor.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/entity_io_mae_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./bounding_box.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./bounding_box.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./gradient_manager.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/root_node.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/root_node.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/entity_io_mmcif_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./module_config.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./module_config.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./transform.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./transform.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/render_mode_node.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_mode_node.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/entity_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./primitives.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./primitives.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/./module_config.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/./module_config.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/pdb_reader.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_reader.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./povray_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/render_modes_node.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_modes_node.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/entity_io_pdb_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./povray.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/pdb_writer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_writer.hh [ 1%] Built target ost_mol_headers cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/scene_node.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./exporter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/entity_io_sdf_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/scene_win.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./exporter_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/sdf_reader.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_reader.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/scene_win_model.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./gost_exporter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./color_ops/map_handle_color_op.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/messages/message_widget.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_widget.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/sdf_writer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_writer.hh In file included from /build/reproducible-path/openstructure-2.6.1/modules/geom/src/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/geom/src/composite2.cc:23: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/geom/src/def.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/geom/src/composite2.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/messages/message_box_widget.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_box_widget.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./map_iso.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/save_entity.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./save_entity.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/messages/log_reader.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/log_reader.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/load_entity.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_entity.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./map_slab.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_slab.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/surface_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/./map_iso_prop.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/argand.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/argand.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/load_surface.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_surface.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh [ 1%] Built target ost_gfx_headers cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/surface_io_msms_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/pdb_str.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_str.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/sdf_str.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_str.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/draw_overlay.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/draw_overlay.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/mmcif_str.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_str.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/drawing_functions.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/drawing_functions.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/stereochemical_params_reader.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/fft_panel.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/fft_panel.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./mol/omf.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./omf.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./seq/sequence_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/info_panel.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/info_panel.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./seq/fasta_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/img2qt.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/img2qt.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/mask_overlay.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/mask_overlay.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./seq/pir_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pir_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/null_overlay.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/null_overlay.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./seq/promod_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./promod_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/overlay.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./seq/profile_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./profile_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/overlay_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./seq/hhm_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/overlay_base_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./seq/pssm_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/overlay_manager.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./seq/clustal_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./clustal_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/overlay_manager_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/overlay_manager_gui.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_gui.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./seq/load.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/overlay_manager_observer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_observer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./seq/save.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./save.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/load_map.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./load_map.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/pointlist_overlay.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh In file included from /build/reproducible-path/openstructure-2.6.1/modules/geom/src/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/geom/src/composite2_op.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/geom/src/composite2_op.cc:24: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/geom/src/composite2_op.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/pointlist_overlay_base.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay_base.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/map_io_df3_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_df3_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/image_format.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./image_format.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/strategies.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/map_io_dx_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dx_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/strategies_fw.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies_fw.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/map_io_spi_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_spi_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/viewer_normalizer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/viewer_normalizer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/map_io_situs_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_situs_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./file_browser.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_browser.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/map_io_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./file_type_dialog.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_type_dialog.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./file_viewer.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_viewer.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/map_io_mrc_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_mrc_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./gl_canvas.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_canvas.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/map_io_dat_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dat_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./gl_win.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_win.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/map_io_ipl_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_ipl_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./scene_menu.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_menu.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/map_io_jpk_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_jpk_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./gosty_app.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./gosty_app.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./admin.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./admin.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/map_io_nanoscope_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_nanoscope_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./module_config.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./module_config.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/map_io_png_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./main.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/map_io_dm3_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dm3_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./main_area.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_area.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/map_io_tiff_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_tiff_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./perspective.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./perspective.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/tiff_util.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./tiff_util.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./scene_selection.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_selection.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/io/src/./img/jpk_util.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/./jpk_util.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./main_window.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_window.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./dock_widget.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh [ 1%] Built target ost_io_headers cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./dock_widget.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./thin_splitter.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./thin_splitter.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./widget.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./widget_geom_handler.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_geom_handler.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./widget_pool.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_pool.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./widget_registry.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_registry.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./widget_state_saver.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_state_saver.hh cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gui/src/./file_loader.hh /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_loader.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 1%] Built target ost_gui_headers [ 1%] Linking CXX shared library ../../../stage/lib/libost_geom.so cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_geom.so.2.6 -o ../../../stage/lib/libost_geom.so.2.6.1 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_geom.so.2.6.1 ../../../stage/lib/libost_geom.so.2.6 ../../../stage/lib/libost_geom.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 1%] Built target ost_geom make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/depend make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu 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-I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_composite2_op.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_mat2.cc [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat3.cc.o [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_mat3.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -c /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_composite3_op.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat4.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_mat4.cc [ 5%] Linking CXX shared library ../../../stage/lib/libost_base.so cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_base.so.2.6 -o ../../../stage/lib/libost_base.so.2.6.1 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_base.so.2.6.1 ../../../stage/lib/libost_base.so.2.6 ../../../stage/lib/libost_base.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 5%] Built target ost_base make -f 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/usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/info/src/info_impl.cc [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_handle.cc.o [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_group.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/info/src/info_handle.cc [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_set.cc.o [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_path.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/info/src/info_item.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/info/src/info_group.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/info/src/info_path.cc [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_visitor.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/info/src/info_set.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/info/src/info_visitor.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/info/src/info_verbose_visitor.cc [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/info/src/geom_info_conversion.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_composite3_op.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_composite3_op.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_vecmat4_op.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_vecmat4_op.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/geom_info_conversion.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_handle.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_impl.cc:37: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_impl.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_handle.cc:30: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_handle.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/wrap_geom.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/wrap_geom.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_quat.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_quat.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_verbose_visitor.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_verbose_visitor.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_item.cc:31: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_item.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_vec3.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_vec3.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_group.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_handle.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_set.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_set.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/info/src/info_set.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_vec2.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_vec2.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_composite3.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_composite3.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_vec4.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_vec4.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_composite2.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_composite2.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_vecmat3_op.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_vecmat3_op.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_mat2.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_mat2.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_composite2_op.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_composite2_op.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_mat3.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_mat3.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_mat4.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_mat4.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_vecmat2_op.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/export_vecmat2_op.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 5%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/geom/_ost_geom.so cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/pymod && /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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 [ 5%] Linking CXX shared library ../../../stage/lib/libost_info.so cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_info.so.2.6 -o ../../../stage/lib/libost_info.so.2.6.1 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 ../../../stage/lib/libost_base.so.2.6.1 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 ../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.6.1/modules/geom/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/geom/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 5%] 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/_ost_base.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 5%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_base_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/base/pymod/wrap_base.cc [ 5%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_base_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/base/pymod/export_logger.cc [ 5%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_base_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/base/pymod/export_range.cc [ 5%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_base_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/base/pymod/export_units.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_info.so.2.6.1 ../../../stage/lib/libost_info.so.2.6 ../../../stage/lib/libost_info.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 5%] 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/img/base/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src 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modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o [ 5%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_algorithm.cc.o [ 5%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/composite_mask.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/chain_base.cc [ 5%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o [ 5%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/circle_mask.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/composite_mask.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/data_algorithm.cc [ 5%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o [ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o [ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_iterator.cc.o [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/data_observer.cc [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o [ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/atom_handle.cc [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o [ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/atom_base.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/atom_view.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/extent_iterator.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/bond_handle.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/extent.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/data.cc [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o [ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/chain_type.cc [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/chain_view.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/extent_mask.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_factory.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/coord_frame.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_handle.cc [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/coord_group.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/editor_base.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_impl.cc [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_list.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_base.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/inverted_mask.cc [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/map.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_handle.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask_base.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_property_mapper.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask_op.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_observer.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_view.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/observable.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_visitor.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/property_id.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/ics_editor.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/not_connected_error.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/extent.cc:31: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/extent.cc:28: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/extent_mask.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/extent_mask.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/extent.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/query.cc [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/query_error.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_factory.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state_fw.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_impl.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_impl.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/polygon_mask.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask.hh:28: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/query_state.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask_base.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask_base.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/observable.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/observable.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/list:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/observable.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/residue_base.cc [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/paste_impl.cc [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask_base.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/composite_mask.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/composite_mask.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/residue_handle.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/circle_mask.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/circle_mask.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/extent_iterator.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/extent_iterator.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask_base.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/inverted_mask.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/inverted_mask.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/in_mem_coord_source.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/coord_group.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/coord_group.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/in_mem_coord_source.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/coord_frame.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/coord_frame.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/data.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/data.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_factory.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_factory.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_factory.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask_base.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/composite_mask.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask_op.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/scoped_ptr.hpp:23, from /usr/include/boost/scoped_ptr.hpp:13, from /usr/include/boost/smart_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask_base_fw.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask_op.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask_op.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/ics_editor.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/ics_editor.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/ics_editor.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/peak.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/map.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/map.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:32: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/phase.cc.o In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/bond_handle.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/list:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/bond_handle.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/bond_handle.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/phase.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_list.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_list.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_list.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/physical_units.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/physical_units.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/editor_base.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/editor_base.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/editor_base.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/chain_view.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/chain_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/pixel_sampling.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/pixel_sampling.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/chain_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/chain_handle.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/chain_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_handle.hh:38, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/data_observer.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/data_observer.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/data_observer.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/editor_base.cc:22: /build/reproducible-path/openstructure-2.6.1/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++/13/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/residue_view.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/residue_view.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/chain_base.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/chain_base.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/chain_base.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/point_list.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_handle.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_handle.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_base.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_base.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_base.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_property_mapper.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_property_mapper.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_property_mapper.hh:28: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/surface_builder.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/surface_builder.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41: /build/reproducible-path/openstructure-2.6.1/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{ | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_handle.hh:38, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_handle.cc:31: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_handle.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/atom_base.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/atom_base.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/atom_base.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/point.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.cc In file included from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/ics_editor.cc:24: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.hh:41: /build/reproducible-path/openstructure-2.6.1/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++/13/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/surface_handle.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/surface_handle.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/atom_view.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/progress.cc In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/atom_view.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/atom_view.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/polygon_mask.cc /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/chain_handle.cc:24: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/atom_handle.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/atom_handle.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/atom_handle.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/size.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/size.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/spherical_mask.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/transfer_connectivity.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_view.cc:30: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_view.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask_info_convert.cc In file included from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_view.cc:40: /build/reproducible-path/openstructure-2.6.1/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++/13/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_state/image_state_factory.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_factory.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/torsion_handle.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/query_view_wrapper.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/view_op.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/view_op.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/coord_source.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/in_mem_coord_source.cc [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/index.cc [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_base.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/query_state.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/pixel_sampling.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/pixel_sampling.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/query_state.cc:24: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/residue_base.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/residue_base.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/bounding_box.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/bounding_box.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/peak.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/peak.cc:30: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/peak.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/xcs_editor.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/xcs_editor.cc [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/src/raster_image/raster_image.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_algorithm.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/paste_impl.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/paste_impl.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:32: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/query.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/query.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.cc:31: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/impl/atom_impl.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/atom_impl.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/polygon_mask.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/polygon_mask.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/polygon_mask.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/impl/chain_impl.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/chain_impl.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/residue_handle.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/impl/connector_impl.cc.o In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/residue_handle.cc:26: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/connector_impl.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point_list.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point_list.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/size.cc:32: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/size.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/spherical_mask.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/spherical_mask.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/impl/dihedral.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/dihedral.cc [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/residue_view.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/residue_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/fragment_impl.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_factory.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_factory.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data_types.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_factory.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/query_ast.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/surface_handle.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/query_impl.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask_info_convert.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/deque:62, from /usr/include/c++/13/stack:62, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/mask_info_convert.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/residue_impl.cc /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/surface_handle.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/surface_builder.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/surface_builder.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/surface_builder.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/surface_impl.cc [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/torsion_impl.cc [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/atom_prop.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/torsion_handle.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/torsion_handle.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/torsion_handle.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/transfer_connectivity.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/transfer_connectivity.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/transfer_connectivity.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/query_view_wrapper.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/query_view_wrapper.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/in_mem_coord_source.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/in_mem_coord_source.cc:1: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/xcs_editor.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/xcs_editor.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/view_op.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/view_op.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/view_op.cc:27: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_base.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_base_fw.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/image_state/image_state_base.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/xcs_editor.cc:26: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/coord_source.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/coord_source.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/connector_impl.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/connector_impl.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/connector_impl.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/atom_impl.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/chain_impl.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/chain_impl.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/connector_impl.cc:24: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/raster_image/raster_image.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/raster_image/raster_image.cc:38: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/src/raster_image/raster_image.cc:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/fragment_impl.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/fragment_impl.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.cc:35: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/chain_impl.cc:23: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/atom_impl.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/atom_impl.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/atom_impl.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/dihedral.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:17, from /usr/include/boost/smart_ptr/enable_shared_from_this.hpp:17, from /usr/include/boost/enable_shared_from_this.hpp:16, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/atom_impl.cc:27: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.cc:40: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/dihedral.cc:21: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/torsion_impl.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/torsion_impl.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/surface_impl.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/bounding_box.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, 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/reproducible-path/openstructure-2.6.1/modules/mol/base/src/bounding_box.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/query_impl.hh:36, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/query_impl.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/query_impl.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/torsion_impl.cc:27: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/residue_impl.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/residue_impl.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/src/impl/residue_impl.cc:25: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 13%] Linking CXX shared library ../../../../stage/lib/libost_img.so cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_img.so.2.6 -o ../../../../stage/lib/libost_img.so.2.6.1 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.6.1 ../../../../stage/lib/libost_base.so.2.6.1 ../../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img.so.2.6.1 ../../../../stage/lib/libost_img.so.2.6 ../../../../stage/lib/libost_img.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 13%] 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 13%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/anisotropic.cc [ 13%] Building CXX object 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-ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/density_slice.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS 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/build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/dft.cc [ 13%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o [ 13%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o [ 13%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/cross_correlate.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB 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/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/fft.cc [ 15%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB 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-ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/gaussian_gradient_magnitude.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS 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modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/line_iterator.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 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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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/gaussian_laplacian.cc [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/histogram.cc.o [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/correlate.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/normalizer_factory.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/norm_log.cc [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer.cc.o [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/fourier_filters.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/histogram.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK 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-isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/norm_od.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/power_spectrum.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/normalizer.cc [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/alg_mirror.cc [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/randomize.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/smooth_mask_image.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/discrete_shrink.cc [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/stat.cc [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/alg_transform.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/alg_shift.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/threshold.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/transformations.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/stat_min_max.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/rscrosscorr.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/polar.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/transformation_base.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/fractional_shift.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/src/line_average.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/transformation_base.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/transformations.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/transformations.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/transformations.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/dft.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/dft.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/gaussian_laplacian.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/gaussian_laplacian.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/gaussian_laplacian.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/norm_od.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/norm_od.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/polar.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/polar.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/polar.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/transformation_base.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/transformation_base.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/stat.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/histogram.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/histogram.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/transformation_base.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/cross_correlate.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/cross_correlate.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/line_iterator.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/line_iterator.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/norm_log.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/norm_log.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/alg_mirror.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/alg_mirror.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/discrete_shrink.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/discrete_shrink.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/discrete_shrink.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/fft.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/power_spectrum.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/power_spectrum.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/alg_shift.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/alg_shift.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/highest_peak_search_3d.cc:4: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/highest_peak_search_3d.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/gaussian.hh:36, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/anisotropic.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/anisotropic.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/anisotropic.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/gaussian_gradient_magnitude.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/gaussian_gradient_magnitude.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/gaussian_gradient_magnitude.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/randomize.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/randomize.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/mask_image.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/threshold.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/threshold.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/fft.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/auto_correlate.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/auto_correlate.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/fft.cc:36: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/fft.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/smooth_mask_image.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/density_slice.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/density_slice.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/correlate.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/correlate.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/normalizer.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/normalizer.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/alg_transform.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/alg_transform.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/fractional_shift.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/fractional_shift.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/local_sigma_threshold.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/local_sigma_threshold.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/local_sigma_threshold.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/stat_min_max.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/stat_min_max.cc:32: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/stat_min_max.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/fourier_filters.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/fourier_filters.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/norm_linear.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/norm_linear.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/rscrosscorr.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/line_average.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/line_average.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/convolute.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/convolute.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/gaussian.hh:36, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/gaussian.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/gaussian.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat_min_max.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/normalizer_factory.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/stat.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/stat.cc:32: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/src/stat.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 17%] Linking CXX shared library ../../../../stage/lib/libost_img_alg.so cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_img_alg.so.2.6 -o ../../../../stage/lib/libost_img_alg.so.2.6.1 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/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.2.6.1 ../../../../stage/lib/libost_info.so.2.6.1 ../../../../stage/lib/libost_base.so.2.6.1 ../../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img_alg.so.2.6.1 ../../../../stage/lib/libost_img_alg.so.2.6 ../../../../stage/lib/libost_img_alg.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 17%] Built target ost_img_alg [ 17%] Linking CXX shared library ../../../../stage/lib/libost_mol.so cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol.so.2.6 -o ../../../../stage/lib/libost_mol.so.2.6.1 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.6.1 ../../../../stage/lib/libost_base.so.2.6.1 ../../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol.so.2.6.1 ../../../../stage/lib/libost_mol.so.2.6 ../../../../stage/lib/libost_mol.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 17%] 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 17%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_op.cc.o [ 17%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o [ 17%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB 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/usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/seq/base/src/sequence_handle.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/seq/base/src/sequence_list.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/seq/base/src/alignment_handle.cc [ 18%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o [ 18%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o [ 18%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/views_from_sequences.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/seq/base/src/profile_handle.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/seq/base/src/views_from_sequences.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/seq/base/src/aligned_region.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/alignment_handle.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/alignment_handle.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/alignment_handle.cc:27: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/alignment_handle.cc:32: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/views_from_sequences.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/views_from_sequences.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/integrity_error.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/views_from_sequences.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/sequence_list.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/sequence_list.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/impl/sequence_list_impl.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_handle.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/sequence_handle.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/sequence_handle.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/sequence_op.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/sequence_op.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/impl/sequence_impl.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /usr/include/boost/format.hpp:17, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/impl/sequence_impl.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/sequence_list.cc:31: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/aligned_region.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/integrity_error.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/src/aligned_region.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27: /build/reproducible-path/openstructure-2.6.1/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, int>::mapped_type' {aka 'int'} [-Wsign-compare] 1607 | else if (atom_site_pos==_atom_site["Cartn_y"]) /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/TMalign.h:1610:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'std::map, int>::mapped_type' {aka 'int'} [-Wsign-compare] 1610 | else if (atom_site_pos==_atom_site["Cartn_z"]) /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/TMalign.h:1653:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1653 | for (i=1;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1655 | for (i=1;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1716 | for (int p=0;p >&, const std::vector >&, std::string, std::string, int, int, double, int, double, double, double)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/TMalign.h:1855:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1855 | for (i=1;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1857 | for (i=1;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2162 | if (!mm_opt) for (i=1;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2372 | for (i=1;i >, double, double, int, int, bool, bool, bool, int, double)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/TMalign.h:3289:12: warning: variable 'Lnorm_d0' set but not used [-Wunused-but-set-variable] 3289 | double Lnorm_d0; | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/TMalign.h: In function 'int CPalign_main(double**, double**, const char*, const char*, const char*, const char*, double*, double (*)[3], double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, std::string&, std::string&, std::string&, double&, int&, double&, double&, double&, int&, int&, int, int, std::vector >, double, double, int, int, bool, bool, bool, int, double)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/TMalign.h:3467:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 3467 | for (i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 3572 | for (i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 3606 | for (r=0;r >&, double, double, bool, bool, int, bool, int, int, int*, int)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/se.h:52:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 52 | for (int r=0;r::size_type' {aka 'long unsigned int'} [-Wsign-compare] 222 | for (int r=0;r > >, std::string)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/MMalign.h:670:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (chain_i=0;chain_i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 673 | for (a=0;a >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 687 | for (a=0;a >&, int, int, int, std::string, int, double**, const std::string&)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/MMalign.h:1010:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1010 | for (a=0;a > >&, const std::vector > >&, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, double**, double**, char*, char*, char*, char*, int, int, std::vector > >&, std::vector > >&, int*, int*, std::vector >&)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/MMalign.h:1166:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1166 | for (i=0;i >&, std::vector > >&, std::vector > >&, int*, int*, double**, std::vector > >&, std::vector > >&, int*, int*, double**)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/MMalign.h:1590:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1590 | for (i=0;i >, double, double, int, int, bool, bool, bool, int, double)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/MMalign.h:2528:12: warning: variable 'Lnorm_d0' set but not used [-Wunused-but-set-variable] 2528 | double Lnorm_d0; | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/MMalign.h: In function 'void MMalign_dimer(double&, const std::vector > >&, const std::vector > >&, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, double**, double**, char*, char*, char*, char*, int, int, int, int, double**, std::vector > >&, std::vector > >&, int*, int*, std::vector >&, double, bool)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/MMalign.h:2680:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2680 | for (c=0;c > >&, std::vector >&, std::vector&, std::vector >&, std::vector&, const std::string&, std::string)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/MMalign.h:2979:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2979 | for (c=0;c >&, const std::vector >&, double**, int*)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/MMalign.h:3016:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 3016 | for (i=0;i struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/entropy.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/db/src/extract_data_helper.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/entropy.cc:24: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 22%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/_ost_base.so cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_base.dir/link.txt --verbose=1 In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/conservation.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_base.so.2.6.1 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/contact_prediction_score.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/hmm_pseudo_counts.cc: In static member function 'static ost::seq::alg::ContextProfileDBPtr ost::seq::alg::ContextProfileDB::FromCRF(const String&)': /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/hmm_pseudo_counts.cc:146:56: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 146 | if(boost::iequals(".gz", boost::filesystem::extension(filename))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/hmm_pseudo_counts.cc:4: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/sequence_identity.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/semiglobal_align.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/bindings/wrap_tmalign.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/wrap_tmalign.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh: At global scope: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/param_set.h:6: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/distance_map.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/impl/align_impl.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/local_align.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/local_align.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/ins_del.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/clip_alignment.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/clip_alignment.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/clip_alignment.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/merge_pairwise_alignments.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/merge_pairwise_alignments.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/merge_pairwise_alignments.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/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{ | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/distance_map.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/distance_map.cc:25: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/variance_map.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/variance_map.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.6.1/modules/base/pymod/settings.py\",\"/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./settings.pyc\",\"settings.py\",doraise=True)" In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/sequence_similarity.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.6.1/modules/base/pymod/stutil.py\",\"/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./stutil.pyc\",\"stutil.py\",doraise=True)" In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/distance_map.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/variance_map.cc:31: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/global_align.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.6.1/modules/base/pymod/table_selector.py\",\"/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./table_selector.pyc\",\"table_selector.py\",doraise=True)" In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/hmm_score.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/hmm_score.cc:1: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/profile_handle.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/hmm_score.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.6.1/modules/base/pymod/xmlrunner.py\",\"/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./xmlrunner.pyc\",\"xmlrunner.py\",doraise=True)" In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.6.1/modules/base/pymod/testutils.py\",\"/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./testutils.pyc\",\"testutils.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 22%] 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/info/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 22%] Building CXX object modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_info_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/info/pymod/wrap_info.cc In file included from /usr/include/c++/13/string:54, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:31, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:27: In member function 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:34, from /build/reproducible-path/openstructure-2.6.1/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 member function '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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/string:42: 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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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); | ^~~~ [ 22%] Linking CXX shared library ../../../stage/lib/libost_db.so cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_db.so.2.6 -o ../../../stage/lib/libost_db.so.2.6.1 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../stage/lib/libost_mol.so.2.6.1 ../../../stage/lib/libost_info.so.2.6.1 ../../../stage/lib/libost_base.so.2.6.1 ../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_db.so.2.6.1 ../../../stage/lib/libost_db.so.2.6 ../../../stage/lib/libost_db.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 22%] 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/conop/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 22%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/conop.cc.o [ 22%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib_base.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/conop/src/compound_lib_base.cc [ 23%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/processor.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK 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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/reproducible-path/openstructure-2.6.1/modules/conop/src/conop.cc [ 23%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/amino_acids.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/conop/src/amino_acids.cc [ 23%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB 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-MF CMakeFiles/ost_conop.dir/processor.cc.o.d -o CMakeFiles/ost_conop.dir/processor.cc.o -c /build/reproducible-path/openstructure-2.6.1/modules/conop/src/processor.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/conop/src/compound.cc [ 23%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/conop/src/model_check.cc [ 23%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/diag.cc.o [ 23%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/conop/src/minimal_compound_lib.cc [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/ring_finder.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB 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/usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/conop/src/heuristic.cc [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/rule_based.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/conop/src/compound_lib.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/conop/src/ring_finder.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/conop/src/rule_based.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/diag.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/diag.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/diag.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/compound_lib_base.hh:5, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/compound_lib_base.cc:1: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/compound.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/compound_lib_base.hh:4: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/rule_based.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/rule_based.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/heuristic.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/heuristic.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/ring_finder.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/processor.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/processor.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/model_check.hh:4, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/model_check.cc:1: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/model_check.cc:2: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/set:62, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/amino_acids.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/compound_lib.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/conop.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/conop.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/compound_lib_base.hh:5, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/minimal_compound_lib.hh:5, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/minimal_compound_lib.cc:1: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/compound.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/conop/src/compound_lib_base.hh:4: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/13/string:54, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/complex:45, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:24: In member function 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]' at /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.6.1/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 member function '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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]' at /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/ios:42: 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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]' at /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/conop/src/ring_finder.cc:93:21: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/conop/src/ring_finder.cc:93:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/conop/src/ring_finder.cc:93:21: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/conop/src/ring_finder.cc:121:23: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/conop/src/ring_finder.cc:121:23: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/conop/src/ring_finder.cc:121:23: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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 file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/info/pymod/wrap_info.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/info/pymod/wrap_info.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Linking CXX shared library ../../../../stage/lib/libost_seq_alg.so cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_seq_alg.so.2.6 -o ../../../../stage/lib/libost_seq_alg.so.2.6.1 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.6.1 ../../../../stage/lib/libost_info.so.2.6.1 ../../../../stage/lib/libost_base.so.2.6.1 ../../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_seq_alg.so.2.6.1 ../../../../stage/lib/libost_seq_alg.so.2.6 ../../../../stage/lib/libost_seq_alg.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 25%] Built target ost_seq_alg /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/NWalign.h: In function 'int extract_aln_from_resi(std::vector >&, char*, char*, std::vector >, std::vector >, std::vector, std::vector, int, int, int)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/NWalign.h:686:21: warning: 'invmap' may be used uninitialized [-Wmaybe-uninitialized] 686 | NWalign_main(seqx, seqy, xlen, ylen, sequence[0],sequence[1], | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 687 | mol_type, invmap, 0, glocal); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/NWalign.h:676:14: note: 'invmap' was declared here 676 | int *invmap; | ^~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/MMalign.h: In function 'int trimComplex(std::vector > >&, std::vector >&, std::vector >&, std::vector&, const std::vector > >&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, int, int)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/MMalign.h:2941:43: warning: 'dinter' may be used uninitialized [-Wmaybe-uninitialized] 2941 | dinter_vec.push_back(make_pair(dinter,r1)); | ~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/MMalign.h:2894:12: note: 'dinter' was declared here 2894 | double dinter; | ^~~~~~ [ 25%] Linking CXX shared library ../../../stage/lib/libost_conop.so cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_conop.so.2.6 -o ../../../stage/lib/libost_conop.so.2.6.1 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_db.so.2.6.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.6.1 ../../../stage/lib/libost_mol.so.2.6.1 ../../../stage/lib/libost_info.so.2.6.1 ../../../stage/lib/libost_base.so.2.6.1 ../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/NWalign.h: In function 'int extract_aln_from_resi(std::vector >&, char*, char*, std::vector >, std::vector >, int)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/NWalign.h:545:21: warning: 'invmap' may be used uninitialized [-Wmaybe-uninitialized] 545 | NWalign_main(seqx, seqy, xlen, ylen, sequence[0],sequence[1], | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 546 | mol_type, invmap, 0, glocal); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/USalign/NWalign.h:535:14: note: 'invmap' was declared here 535 | int *invmap; | ^~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_conop.so.2.6.1 ../../../stage/lib/libost_conop.so.2.6 ../../../stage/lib/libost_conop.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 25%] Built target ost_conop make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/depend make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/gfx/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/build [ 25%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem 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/build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/clash_score.cc [ 27%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o [ 27%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o [ 26%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o [ 27%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o [ 27%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/distance_test_common.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/superpose_frames.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB 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CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o.d -o CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -c /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/filter_clashes.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/construct_cbeta.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o [ 27%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.cc.o [ 27%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-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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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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/consistency_checks.cc [ 27%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS 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modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG 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modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/color.cc [ 28%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && 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/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_prim.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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-ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/domain_find.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG 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/build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/similarity_matrix.cc [ 28%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK 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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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/sec_struct.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/symmetry_node.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/nonstandard.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/molck.cc [ 28%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.cc.o [ 28%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.cc.o [ 28%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/find_membrane.cc [ 28%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/selection.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/entity_to_density.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/biounit.cc.o -MF CMakeFiles/ost_mol_alg.dir/biounit.cc.o.d -o CMakeFiles/ost_mol_alg.dir/biounit.cc.o -c /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/biounit.cc [ 28%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_test_object.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/prim_list.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/scene.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/selection.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/entity.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/surface.cc [ 28%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/gradient.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_prim.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_prim.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_prim.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/similarity_matrix.hh:7, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/similarity_matrix.cc:1: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/similarity_matrix.hh:5: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/symmetry_node.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/symmetry_node.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gl_helper.hh:36, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/symmetry_node.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/primitives.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/primitives.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gl_helper.hh:36, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/primitives.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/gradient_manager.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/sec_structure_segments.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/sec_struct.cc:1: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/vertex_array.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/vertex_array.cc [ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/vertex_array_helper.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/nonstandard.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/nonstandard.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/selection.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/selection.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/adjacency_bitmap.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/trajectory_analysis.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/trajectory_analysis.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/pdbize.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/pdbize.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/molck.cc:1: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/biounit.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/biounit.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/filter_clashes.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/filter_clashes.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/pdbize.hh:25: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mmcif_info.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/biounit.hh:23: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/structure_analysis.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/structure_analysis.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/material.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/material.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/find_membrane.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/find_membrane.cc:1: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/povray.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/povray.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/consistency_checks.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/consistency_checks.cc:20: /usr/include/c++/13/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/gost_exporter.cc.o /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/gost_exporter.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:1: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/distance_test_common.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/distance_test_common.cc:1: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/wrap_tmalign.cc: In function 'ost::bindings::MMAlignResult ost::bindings::WrappedMMAlign(const std::vector&, const std::vector&, const ost::seq::SequenceList&, const ost::seq::SequenceList&, const std::vector&, const std::vector&, bool, const std::map&)': /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/wrap_tmalign.cc:904:36: warning: 'seqx' may be used uninitialized [-Wmaybe-uninitialized] 904 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 905 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 907 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 908 | sequence, d0_scale, fast_opt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/wrap_tmalign.cc:551:11: note: 'seqx' was declared here 551 | char *seqx, *seqy; // for the protein sequence | ^~~~ /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/wrap_tmalign.cc:904:36: warning: 'secx' may be used uninitialized [-Wmaybe-uninitialized] 904 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 905 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 907 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 908 | sequence, d0_scale, fast_opt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/wrap_tmalign.cc:552:11: note: 'secx' was declared here 552 | char *secx, *secy; // for the secondary structure | ^~~~ /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/wrap_tmalign.cc:904:36: warning: 'secy' may be used uninitialized [-Wmaybe-uninitialized] 904 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 905 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 907 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 908 | sequence, d0_scale, fast_opt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/wrap_tmalign.cc:552:18: note: 'secy' was declared here 552 | char *secx, *secy; // for the secondary structure | ^~~~ /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/wrap_tmalign.cc:904:36: warning: 'seqy' may be used uninitialized [-Wmaybe-uninitialized] 904 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 905 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 907 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 908 | sequence, d0_scale, fast_opt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/bindings/src/wrap_tmalign.cc:551:18: note: 'seqy' was declared here 551 | char *seqx, *seqy; // for the protein sequence | ^~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_test_object.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_test_object.cc:31: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/locale:41, from /usr/include/boost/filesystem/detail/path_traits.hpp:18, from /usr/include/boost/filesystem/path.hpp:21, from /usr/include/boost/filesystem/operations.hpp:20, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_test_object.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/construct_cbeta.cc:4: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/local_dist_diff_test.cc:4: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/construct_cbeta.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/local_dist_diff_test.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/prim_list.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/prim_list.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/clash_score.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc:2: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/local_dist_diff_test.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/local_dist_diff_test.cc:6: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/molck.cc:4: /build/reproducible-path/openstructure-2.6.1/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{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc:3: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/scene.cc:40: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/scene.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/distance_rmsd_test.cc:2: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/distance_rmsd_test.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gradient.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gradient.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gradient.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/texture.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/texture.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/collada_exporter.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/collada_exporter.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_node.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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/bind/bind.hpp:26, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_node.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/distance_rmsd_test.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/distance_rmsd_test.cc:3: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/exporter.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object.cc:32: /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/svd_superpose.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object.hh:124:31: warning: 'virtual geom::AlignedCuboid ost::gfx::GfxObj::GetBoundingBox(bool) const' was hidden [-Woverloaded-virtual=] 124 | virtual geom::AlignedCuboid GetBoundingBox(bool use_tf=false) const; | ^~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_test_object.hh:40:31: note: by 'virtual geom::AlignedCuboid ost::gfx::GfxTestObj::GetBoundingBox() const' 40 | virtual geom::AlignedCuboid GetBoundingBox() const; | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/svd_superpose.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/dft.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/entity_to_density.cc:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/entity_to_density.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/color_ops/color_op.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/color_op.cc In file included from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/scene.cc:49: /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object.hh:124:31: warning: 'virtual geom::AlignedCuboid ost::gfx::GfxObj::GetBoundingBox(bool) const' was hidden [-Woverloaded-virtual=] 124 | virtual geom::AlignedCuboid GetBoundingBox(bool use_tf=false) const; | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/scene.cc:50: /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_test_object.hh:40:31: note: by 'virtual geom::AlignedCuboid ost::gfx::GfxTestObj::GetBoundingBox() const' 40 | virtual geom::AlignedCuboid GetBoundingBox() const; | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/entity.cc:36: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/entity.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/surface.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/surface.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ [ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/by_element_color_op.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/superpose_frames.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, 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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/superpose_frames.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/color_ops/by_chain_color_op.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/by_chain_color_op.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gradient_manager.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/locale:41, from /usr/include/boost/filesystem/detail/path_traits.hpp:18, from /usr/include/boost/filesystem/path.hpp:21, from /usr/include/boost/filesystem/operations.hpp:20, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gradient_manager.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/vertex_array_helper.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/vertex_array_helper.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/vertex_array_helper.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/color_ops/uniform_color_op.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/uniform_color_op.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/entity.cc:39: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/entity.cc:52: /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ [ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/gradient_color_op.cc [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/entity_view_color_op.cc In constructor '{anonymous}::ExtendedBridge::ExtendedBridge({anonymous}::ExtendedBridge&&)', inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]' at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]' at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]' at /usr/include/c++/13/bits/vector.tcc:117:30, inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)' at /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/sec_struct.cc:87:33: /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/sec_struct.cc:10:8: warning: '.{anonymous}::ExtendedBridge::parallel' may be used uninitialized [-Wmaybe-uninitialized] 10 | struct ExtendedBridge { | ^~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/sec_struct.cc: In function 'bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)': /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/sec_struct.cc:87:49: note: '' declared here 87 | extended_bridges.push_back(ExtendedBridge()); | ^ In constructor '{anonymous}::ExtendedBridge::ExtendedBridge({anonymous}::ExtendedBridge&&)', inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]' at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]' at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]' at /usr/include/c++/13/bits/vector.tcc:468:28, inlined from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]' at /usr/include/c++/13/bits/vector.tcc:123:21, inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)' at /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/sec_struct.cc:87:33: /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/sec_struct.cc:10:8: warning: '.{anonymous}::ExtendedBridge::parallel' may be used uninitialized [-Wmaybe-uninitialized] 10 | struct ExtendedBridge { | ^~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/sec_struct.cc: In function 'bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)': /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/sec_struct.cc:87:49: note: '' declared here 87 | extended_bridges.push_back(ExtendedBridge()); | ^ In file included from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/surface.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/surface.cc:28: /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/basic_gradient_color_op.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/material.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/material.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/iterator:61, from /usr/include/boost/operators.hpp:98, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color.hh:28: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/povray.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/povray.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/povray.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/domain_find.cc:3: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, 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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/domain_find.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/gradient_level_color_op.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/entity_renderer.cc [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/entity_detail.cc [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/cartoon_renderer.cc [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/custom_renderer.cc [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/cpk_renderer.cc [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/debug_renderer.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/vertex_array.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/vertex_array.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /usr/include/boost/format.hpp:17, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/vertex_array.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/domain_find.cc:9: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/simple_renderer.cc [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/sline_renderer.cc [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/line_trace_renderer.cc [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/backbone_trace.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/by_element_color_op.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/by_element_color_op.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/by_element_color_op.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/impl/connect_renderer_base.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/connect_renderer_base.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gost_exporter.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/gost_exporter.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/by_chain_color_op.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/by_chain_color_op.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/by_chain_color_op.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/color_op.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/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) | ^~~~~~~~~~~~~~ [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/trace_renderer_base.cc [ 32%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/info/_ost_info.so cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/info/_ost_info.so CMakeFiles/_ost_info.dir/wrap_info.cc.o -L/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_info.so.2.6.1 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 ../../../stage/lib/libost_base.so.2.6.1 ../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/mapped_property.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/by_element_color_op.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/entity_view_color_op.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/13/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/impl/tabulated_trig.cc.o /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/tabulated_trig.cc [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/trace_renderer.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/basic_gradient_color_op.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_handle.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/by_chain_color_op.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/uniform_color_op.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/dyn_cast.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/uniform_color_op.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.6.1/modules/info/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/info/./__init__.pyc\",\"__init__.py\",doraise=True)" In file included from /usr/include/c++/13/string:54, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/complex:45, from /build/reproducible-path/openstructure-2.6.1/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>::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++/13/bits/basic_string.h:899:15, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/13/bits/basic_string.h:1079:16: 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] 1079 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_base.hh:25, from /build/reproducible-path/openstructure-2.6.1/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++/13/ios:42: 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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); | ^~~~ make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 32%] 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[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 32%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_atom.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/gradient_color_op.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/impl/fast_spheres.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/fast_spheres.cc.o -MF CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o -c /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/fast_spheres.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/custom_renderer.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/custom_renderer.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/render_options/render_options.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o -c /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/render_options.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/surface.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/basic_gradient_color_op.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/surface.hh:102:8: note: by 'ost::gfx::Surface::Apply' 102 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/cartoon_renderer.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/cartoon_renderer.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/gradient_level_color_op.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/dyn_cast.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/gradient_level_color_op.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake "--color=" [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o In file included from /usr/include/c++/13/string:54: In member function 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/line_render_options.cc In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.6.1/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 member function '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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/ios:42: 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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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); | ^~~~ make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 32%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_data.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_op.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/entity_renderer.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/entity_renderer.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/entity_detail.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_view.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/entity_detail.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 32%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_data_algorithm.cc [ 32%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_extent.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/cpk_renderer.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/cpk_renderer.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/cpk_renderer.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/debug_renderer.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/debug_renderer.cc:19: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/13/string:54: In member function 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.6.1/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 member function '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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/ios:42: 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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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); | ^~~~ [ 32%] Linking CXX shared library ../../../stage/lib/libost_bindings.so cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_bindings.dir/link.txt --verbose=1 In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/sline_renderer.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/sline_renderer.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity_fw.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/sline_renderer.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 32%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom_view.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_atom_view.cc /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_bindings.so.2.6 -o ../../../stage/lib/libost_bindings.so.2.6.1 CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -L/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_seq.so.2.6.1 ../../../stage/lib/libost_mol.so.2.6.1 ../../../stage/lib/libost_info.so.2.6.1 ../../../stage/lib/libost_base.so.2.6.1 ../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 [ 32%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_handle.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_image_handle.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/cpk_renderer.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/connect_renderer_base.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/simple_renderer.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/simple_renderer.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/line_trace_renderer.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/line_trace_renderer.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_bindings.so.2.6.1 ../../../stage/lib/libost_bindings.so.2.6 ../../../stage/lib/libost_bindings.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' In member function 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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); | ^~~~ [ 32%] Built target ost_bindings [ 32%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_bond.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/backbone_trace.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/simple_renderer.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/custom_render_options.cc [ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/cpk_render_options.cc [ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/simple_render_options.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh:35, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/backbone_trace.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/backbone_trace.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ [ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/sline_render_options.cc [ 33%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_peak.cc [ 33%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_phase.cc [ 35%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_point.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/trace_renderer.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/mapped_property.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:28: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_progress.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/trace_renderer_base.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/render_options/line_trace_render_options.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/line_trace_render_options.cc [ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_chain.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/fast_spheres.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_raster_image.cc [ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_chain_view.cc [ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_coord_group.cc [ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_coord_frame.cc [ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_editors.cc [ 35%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_size.cc [ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_entity.cc [ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_entity_view.cc [ 35%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_mask.cc [ 35%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_image_list.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/render_options.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/input.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/render_options.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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>::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++/13/bits/basic_string.h:899:15, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/13/bits/basic_string.h:1079:16: 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] 1079 | { 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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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); | ^~~~ [ 35%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_map.cc [ 36%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_property_id.cc [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/cartoon_render_options.cc [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/trace_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o -c /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/render_options/trace_render_options.cc [ 36%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/wrap_img.cc [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/map_handle_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o -c /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/map_handle_color_op.cc [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/map_iso.cc [ 36%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_query.cc [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_slab.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/map_slab.cc In file included from /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/domain_find.cc:363:37: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:109:23: warning: '*(uint64_t*)' may be used uninitialized [-Wmaybe-uninitialized] 109 | data_[byte_index] &= ~(one << bit_index); | ~~~~~~~~~~~~~~~~^ [ 36%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_residue.cc [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_iso_gen.cc [ 36%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_residue_view.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/wrap_extent_iterator.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_extent.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_extent.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 36%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_surface.cc [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_iso_gen_s.cc [ 36%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_bounding_box.cc [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_iso_gen_o.cc [ 37%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_query_view_wrapper.cc In file included from /usr/include/c++/13/string:54, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/complex:45, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:24: In member function 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() 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++/13/bits/basic_string.h:869:23, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/13/bits/basic_string.h:266:17: 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] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.6.1/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 member function '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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/13/ios:42: 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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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); | ^~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_octree.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_data.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_data.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_atom.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_atom.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_data_algorithm.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_data_algorithm.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_image_handle.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_image_handle.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/peak.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_peak.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_peak.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/color_ops/map_handle_color_op.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_atom_view.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_atom_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/discrete_shrink.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/map_iso.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/map_iso.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_iso_gen.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_iso_gen.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/vertex_array.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_iso_prop.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_iso_gen_o.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/shared_array.hpp:21, from /usr/include/boost/shared_array.hpp:17, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_iso_gen_o.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/map_slab.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/map_slab.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_bond.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_bond.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/octree_isocont.cc.o In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point_list.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_point.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_point.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/octree_isocont.cc /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_coord_frame.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_coord_frame.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_size.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_size.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_raster_image.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_raster_image.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_chain.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_chain.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_octree.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_octree.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:32: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_image_list.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_image_list.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_torsion.cc [ 37%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_visitor.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_iso_gen_s.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/shared_array.hpp:21, from /usr/include/boost/shared_array.hpp:17, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/map_iso_gen_s.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/polygon_mask.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/mask.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_mask.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_mask.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/wrap_mol.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_entity.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_entity.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_entity.cc:24: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_query.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_query.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_entity_view.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_entity_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_entity_property_mapper.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_editors.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_editors.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_editors.cc:25: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_map.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/export_map.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/wrap_img.cc:33: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/wrap_img.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_group.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_coord_group.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_coord_group.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_chain_view.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_chain_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_property_id.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_property_id.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_residue.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_residue.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/impl/octree_isocont.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/iterator:61, from /usr/include/boost/container_hash/is_range.hpp:16, from /usr/include/boost/container_hash/hash.hpp:15, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_map.hpp:20, from /usr/include/boost/unordered_map.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_residue_view.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_residue_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_surface.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_surface.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_query_view_wrapper.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_query_view_wrapper.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_bounding_box.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_bounding_box.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_entity_property_mapper.cc:3: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_entity_property_mapper.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_visitor.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/export_visitor.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Linking CXX shared library ../../../../stage/lib/libost_mol_alg.so cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/atom_scattering_properties.txt /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/atom_scattering_properties.txt In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/editor_base.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/wrap_mol.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/wrap_mol.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/stereo_chemical_props.txt /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/stereo_chemical_props.txt cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol_alg.so.2.6 -o ../../../../stage/lib/libost_mol_alg.so.2.6.1 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 CMakeFiles/ost_mol_alg.dir/biounit.cc.o -L/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_img_alg.so.2.6.1 ../../../../stage/lib/libost_seq_alg.so.2.6.1 ../../../../stage/lib/libost_conop.so.2.6.1 ../../../../stage/lib/libost_img.so.2.6.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_db.so.2.6.1 ../../../../stage/lib/libost_seq.so.2.6.1 ../../../../stage/lib/libost_mol.so.2.6.1 ../../../../stage/lib/libost_info.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_base.so.2.6.1 ../../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol_alg.so.2.6.1 ../../../../stage/lib/libost_mol_alg.so.2.6 ../../../../stage/lib/libost_mol_alg.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 38%] 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/io/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src/CMakeFiles/ost_io.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 38%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_utils.cc.o [ 38%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/convert.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/convert.cc [ 40%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_manager.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/io_utils.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/io_manager.cc [ 40%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o [ 40%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o [ 40%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_crd_handler.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK 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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/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_sdf_handler.cc [ 41%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o [ 41%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/mol/save_entity.cc cd 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-DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/mol/mmcif_reader.cc [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/mol/mmcif_info.cc [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/mol/stereochemical_params_reader.cc [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/mol/omf.cc [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/seq/clustal_io_handler.cc [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/load.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/seq/load.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/io_profile.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/io_profile.cc:1: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/io_profile.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/mmcif_info.cc:21: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_exception.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/mmcif_info.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/stereochemical_params_reader.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/stereochemical_params_reader.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/locale:41, from /usr/include/boost/filesystem/detail/path_traits.hpp:18, from /usr/include/boost/filesystem/path.hpp:21, from /usr/include/boost/filesystem/fstream.hpp:17, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/stereochemical_params_reader.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/surface_io_handler.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/surface_io_msms_handler.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/surface_io_msms_handler.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/surface_io_msms_handler.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/save.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/seq/save.cc /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/surface_io_msms_handler.cc: In function 'std::pair ost::io::{anonymous}::detect_files(const boost::filesystem::path&)': /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/surface_io_msms_handler.cc:36:45: warning: 'boost::filesystem::path boost::filesystem::change_extension(const path&, const path&)' is deprecated: Use path::replace_extension() instead [-Wdeprecated-declarations] 36 | return std::make_pair(bf::change_extension(loc, ".vert"), | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/surface_io_msms_handler.cc:25: /usr/include/boost/filesystem/convenience.hpp:41:13: note: declared here 41 | inline path change_extension(const path& p, const path& new_extension) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/surface_io_msms_handler.cc:37:45: warning: 'boost::filesystem::path boost::filesystem::change_extension(const path&, const path&)' is deprecated: Use path::replace_extension() instead [-Wdeprecated-declarations] 37 | bf::change_extension(loc, ".face")); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/boost/filesystem/convenience.hpp:41:13: note: declared here 41 | inline path change_extension(const path& p, const path& new_extension) | ^~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/mmcif_reader.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/profile.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/mmcif_reader.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/save_entity.cc:20: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/save_entity.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 42%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/img/_ost_img.so cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img.dir/link.txt --verbose=1 In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/load_surface.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_str.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/mmcif_str.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/mmcif_str.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/load_surface.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_img.so.2.6.1 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../stage/lib/libost_info.so.2.6.1 ../../../../stage/lib/libost_base.so.2.6.1 ../../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mmcif_reader.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_str.hh:25: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/dcd_io.cc:33: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/dcd_io.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/mmcif_reader.cc:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_str.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_str.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/load_entity.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/load_entity.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_str.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/sdf_str.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/sdf_str.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/chemdict_parser.cc:1: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chem_class.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/load_entity.cc:24: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_writer.cc:35: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/locale:41, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_writer.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/io_manager.cc:19: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_pdb_handler.cc:35: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_pdb_handler.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_str.cc:22: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/load_surface.cc:23: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/seq/fasta_io_handler.cc /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_writer.cc: In constructor 'ost::io::PDBWriter::PDBWriter(const boost::filesystem::path&, const ost::io::IOProfile&)': /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_writer.cc:395:58: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 395 | if (boost::iequals(".pqr", boost::filesystem::extension(filename))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_writer.cc:28: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_writer.cc:398:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 398 | if (boost::iequals(".gz", boost::filesystem::extension(filename))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_writer.cc: In constructor 'ost::io::PDBWriter::PDBWriter(const String&, const ost::io::IOProfile&)': /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_writer.cc:412:58: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 412 | if (boost::iequals(".pqr", boost::filesystem::extension(filename))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_writer.cc:415:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 415 | if (boost::iequals(".gz", boost::filesystem::extension(filename))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/omf.cc:4: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/omf.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_mmcif_handler.cc:35: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_mmcif_handler.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 42%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/seq/pir_io_handler.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25: /build/reproducible-path/openstructure-2.6.1/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++/13/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/seq/promod_io_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/seq/promod_io_handler.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/load.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/load.cc:19: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/load.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/dcd_io.cc:40: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.6.1/modules/img/base/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/img/./__init__.pyc\",\"__init__.py\",doraise=True)" In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh:35, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_sdf_handler.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_sdf_handler.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mmcif_info.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/omf.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/omf.cc:8: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 43%] Built target _ost_img In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/sdf_reader.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, 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/reproducible-path/openstructure-2.6.1/modules/io/src/mol/sdf_reader.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/seq/hhm_io_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/seq/hhm_io_handler.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/sdf_reader.cc: In member function 'void ost::io::SDFReader::ClearState(const boost::filesystem::path&)': /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/sdf_reader.cc:123:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 123 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/sdf_reader.cc:24: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/clustal_io_handler.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/clustal_io_handler.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 43%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/wrap_alg.cc /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_pdb_handler.cc: In member function 'virtual void ost::io::EntityIOPDBHandler::Export(const ost::mol::EntityView&, const boost::filesystem::path&) const': /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_pdb_handler.cc:52:50: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 52 | if (boost::iequals(boost::filesystem::extension(loc), ".pqr")) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_pdb_handler.cc:27: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/sdf_writer.hh:35, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/sdf_writer.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/sdf_writer.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/clustal_io_handler.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/clustal_io_handler.cc:29: /build/reproducible-path/openstructure-2.6.1/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 /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_crd_handler.cc:33: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_crd_handler.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_reader.cc:32: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /usr/include/boost/iostreams/filter/gzip.hpp:21, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_reader.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/omf.cc: In function 'void {anonymous}::DumpName(std::ostream&, const String&)': /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/omf.cc:2047:43: warning: the address of 'static constexpr unsigned char std::numeric_limits::max()' will never be NULL [-Waddress] 2047 | ss << std::numeric_limits::max << ". "; | ^~~ In file included from /usr/include/c++/13/bits/specfun.h:44, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/omf.cc:3: /usr/include/c++/13/limits:598:7: note: 'static constexpr unsigned char std::numeric_limits::max()' declared here 598 | max() _GLIBCXX_USE_NOEXCEPT { return __SCHAR_MAX__ * 2U + 1; } | ^~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_pqr_handler.cc:35: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_pqr_handler.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_crd_handler.cc: In constructor 'ost::io::CRDReader::CRDReader(const boost::filesystem::path&)': /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_crd_handler.cc:63:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 63 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_crd_handler.cc:27: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_reader.cc:35: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/save.cc:22: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/save.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_reader.cc: In member function 'void ost::io::PDBReader::Init(const boost::filesystem::path&)': /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_reader.cc:91:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 91 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_reader.cc:20: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_pqr_handler.cc: In constructor 'ost::io::PQRReader::PQRReader(const boost::filesystem::path&)': /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_pqr_handler.cc:61:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 61 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_pqr_handler.cc:28: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/pdb_reader.cc:97:49: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 97 | if(boost::iequals(boost::filesystem::extension(loc), ".pqr")) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_mae_handler.cc:38: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_mae_handler.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 43%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/export_filter.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 45%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/export_normalizer.cc /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_mae_handler.cc: In constructor 'ost::io::MAEReader::MAEReader(const boost::filesystem::path&)': /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_mae_handler.cc:60:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 60 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/io/src/mol/entity_io_mae_handler.cc:31: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ [ 45%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/export_transcendentals.cc [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/seq/pssm_io_handler.cc [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/load_map.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/img/load_map.cc [ 45%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/export_polar.cc [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_dx_handler.cc [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_spi_handler.cc [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_situs_handler.cc [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_mrc_handler.cc [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_dm3_handler.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/promod_io_handler.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/promod_io_handler.cc:22: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/hhm_io_handler.cc: In member function 'virtual void ost::io::HhmIOHandler::Import(ost::seq::ProfileHandle&, const boost::filesystem::path&)': /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/hhm_io_handler.cc:133:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 133 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/hhm_io_handler.cc:27: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/fasta_io_handler.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/fasta_io_handler.cc:19: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/fasta_io_handler.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_tiff_handler.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_dat_handler.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/pir_io_handler.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/pir_io_handler.cc:19: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/pir_io_handler.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/img/map_io_ipl_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_ipl_handler.cc /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/pssm_io_handler.cc: In member function 'virtual void ost::io::PssmIOHandler::Import(ost::seq::ProfileHandle&, const boost::filesystem::path&)': /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/pssm_io_handler.cc:47:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 47 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/io/src/seq/pssm_io_handler.cc:27: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_jpk_handler.cc [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_nanoscope_handler.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/load_map.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/load_map.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_dm3_handler.cc:37: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_dm3_handler.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_spi_handler.cc:35: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_spi_handler.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_dat_handler.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/shared_array.hpp:21, from /usr/include/boost/shared_array.hpp:17, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_dat_handler.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/load_map.cc:24: /build/reproducible-path/openstructure-2.6.1/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++/13/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/img/map_io_png_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_png_handler.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_situs_handler.cc:34: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_situs_handler.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_df3_handler.cc /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_tiff_handler.cc:33: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_tiff_handler.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_dx_handler.cc:37: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_dx_handler.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/img/image_format.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/img/image_format.cc [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/tiff_util.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/io/src/img/tiff_util.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_ipl_handler.cc:31: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_ipl_handler.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_dx_handler.cc: In member function 'virtual void ost::io::MapIODxHandler::Import(ost::img::MapHandle&, const boost::filesystem::path&, const ost::io::ImageFormatBase&)': /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_dx_handler.cc:97:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 97 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_dx_handler.cc:31: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_mrc_handler.cc:76: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_mrc_handler.cc:58: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/transcendentals.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/export_transcendentals.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/export_transcendentals.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/auto_correlate.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/wrap_alg.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/wrap_alg.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/alg_transform.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/transform.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_jpk_handler.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_jpk_handler.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/gaussian.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/filter.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/export_filter.cc:30: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/export_filter.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Linking CXX shared library ../../../stage/lib/libost_gfx.so In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_nanoscope_handler.cc:34: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/test_texture.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/textures/test_texture.png In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_nanoscope_handler.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/gfx/src/glyph_texture.png /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/textures/glyph_texture.png cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gfx.dir/link.txt --verbose=1 In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_png_handler.cc:34: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_png_handler.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_gfx.so.2.6 -o ../../../stage/lib/libost_gfx.so.2.6.1 CMakeFiles/ost_gfx.dir/bitmap_io.cc.o CMakeFiles/ost_gfx.dir/exporter.cc.o 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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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_conop.so.2.6.1 ../../../stage/lib/libost_img_alg.so.2.6.1 /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.2.6.1 ../../../stage/lib/libost_seq.so.2.6.1 ../../../stage/lib/libost_mol.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img.so.2.6.1 ../../../stage/lib/libost_info.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 ../../../stage/lib/libost_base.so.2.6.1 ../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/polar.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/export_polar.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/export_polar.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/export_normalizer.cc:30: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/img/alg/pymod/export_normalizer.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_df3_handler.cc:34: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/map_io_df3_handler.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/tiff_util.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/tiff_util.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/complex:44, from /build/reproducible-path/openstructure-2.6.1/modules/io/src/img/tiff_util.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_gfx.so.2.6.1 ../../../stage/lib/libost_gfx.so.2.6 ../../../stage/lib/libost_gfx.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 46%] Built target ost_gfx [ 47%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/mol/_ost_mol.so cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol.so.2.6.1 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../stage/lib/libost_info.so.2.6.1 ../../../../stage/lib/libost_base.so.2.6.1 ../../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.6.1/modules/mol/base/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 47%] 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/seq/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 47%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o [ 47%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_sequence.cc.o [ 47%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/seq/base/pymod/export_sequence.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/seq/base/pymod/export_profile_handle.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/seq/base/pymod/wrap_seq.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/pymod/export_sequence.cc:30: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/pymod/export_sequence.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/pymod/export_sequence.cc:34: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/seq/base/pymod/export_sequence.cc:37: /build/reproducible-path/openstructure-2.6.1/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{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/lddt.cc:31: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:27: /build/reproducible-path/openstructure-2.6.1/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++/13/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/sequence_viewer/moc_seq_secstr_painter.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp [ 65%] Linking CXX executable ../../../stage/bin/test_mae_standalone cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mae_standalone.dir/link.txt --verbose=1 In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37: /build/reproducible-path/openstructure-2.6.1/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++/13/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib ../../../stage/lib/libost_io.so.2.6.1 ../../../stage/lib/libost_mol_alg.so.2.6.1 ../../../stage/lib/libost_conop.so.2.6.1 ../../../stage/lib/libost_db.so.2.6.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_seq_alg.so.2.6.1 ../../../stage/lib/libost_seq.so.2.6.1 ../../../stage/lib/libost_mol.so.2.6.1 ../../../stage/lib/libost_img_alg.so.2.6.1 ../../../stage/lib/libost_img.so.2.6.1 ../../../stage/lib/libost_info.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 ../../../stage/lib/libost_base.so.2.6.1 ../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 /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.1.83.0 /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/reproducible-path/openstructure-2.6.1/modules/mol/alg/src/lddt.cc:39: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, 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/reproducible-path/openstructure-2.6.1/tools/molck/main.cc:2: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/observer.hh:33: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.6.1/tools/molck/main.cc:10: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/ff_reader.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' /build/reproducible-path/openstructure-2.6.1/tools/molck/main.cc: In function 'ost::conop::CompoundLibPtr load_compound_lib(const String&)': /build/reproducible-path/openstructure-2.6.1/tools/molck/main.cc:119:48: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 119 | fs::path path_only=path_and_exe.branch_path(); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /build/reproducible-path/openstructure-2.6.1/tools/molck/main.cc:3: /usr/include/boost/filesystem/path.hpp:1129:10: note: declared here 1129 | path branch_path() const { return parent_path(); } | ^~~~~~~~~~~ /build/reproducible-path/openstructure-2.6.1/tools/molck/main.cc:120:48: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 120 | fs::path share_path = path_only.branch_path(); | ~~~~~~~~~~~~~~~~~~~~~^~ /usr/include/boost/filesystem/path.hpp:1129:10: note: declared here 1129 | path branch_path() const { return parent_path(); } | ^~~~~~~~~~~ [ 65%] Built target test_mae_standalone [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/conservation_painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/background_painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/sequence_viewer/moc_sequence_delegate.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/align_properties_painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/sequence_viewer/moc_sequence_model.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/file_type_dialog.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp:10: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/scene_selection.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/sequence_viewer/moc_sequence_table_view.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/file_browser.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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_title_row.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/secstr_row.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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_base_view_object.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/python_shell/moc_main_thread_runner.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_main_thread_runner.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/python_shell/moc_completer_base.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_secstr_painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_selection_painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_text_painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_row.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_search_bar.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp:9: /usr/include/c++/13/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/python_shell/moc_gutter.cpp.o /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_gutter.cpp [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_output_redirector.cpp [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_completer.cpp [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter_worker.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_view_object.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/title_row.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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_namespace_tree_model.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_namespace_tree_model.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_table_view.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/reproducible-path/openstructure-2.6.1/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++/13/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_shell.cpp.o In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/reproducible-path/openstructure-2.6.1/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{ | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell.cpp /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Linking CXX executable ../../../stage/bin/chemdict_tool cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemdict_tool.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o -o ../../../stage/bin/chemdict_tool -L/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_io.so.2.6.1 ../../../stage/lib/libost_mol_alg.so.2.6.1 ../../../stage/lib/libost_conop.so.2.6.1 ../../../stage/lib/libost_db.so.2.6.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_seq_alg.so.2.6.1 ../../../stage/lib/libost_seq.so.2.6.1 ../../../stage/lib/libost_mol.so.2.6.1 ../../../stage/lib/libost_img_alg.so.2.6.1 ../../../stage/lib/libost_img.so.2.6.1 ../../../stage/lib/libost_info.so.2.6.1 ../../../stage/lib/libost_base.so.2.6.1 ../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 /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.1.83.0 /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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/tick_painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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_shell_widget.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/reproducible-path/openstructure-2.6.1/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++/13/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_text_logger.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_state_machine.cpp [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_state.cpp make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 67%] Built target chemdict_tool [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_transition.cpp [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_transition_guard.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/alignment_view_object.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_viewer.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_bar.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/moc_main.cpp:10: /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:40:25: required from here /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/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 | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:30: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:32: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_bar.cpp [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_manager.cpp [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_bottom_bar.cpp [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG 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-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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK 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-I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/panels/../../../../../modules/gui/src/panels/drop_box.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_option_group.cpp [ 71%] Linking CXX executable ../../../../stage/bin/lddt cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_io.so.2.6.1 ../../../../stage/lib/libost_mol_alg.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_seq_alg.so.2.6.1 ../../../../stage/lib/libost_img_alg.so.2.6.1 ../../../../stage/lib/libost_img.so.2.6.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_conop.so.2.6.1 ../../../../stage/lib/libost_db.so.2.6.1 ../../../../stage/lib/libost_seq.so.2.6.1 ../../../../stage/lib/libost_mol.so.2.6.1 ../../../../stage/lib/libost_info.so.2.6.1 ../../../../stage/lib/libost_base.so.2.6.1 ../../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_bar.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_option.cpp make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 71%] Built target lddt [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB 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-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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_widget.cpp cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp [ 71%] Linking CXX executable ../../stage/bin/molck cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../stage/lib/libost_io.so.2.6.1 ../../stage/lib/libost_mol_alg.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../stage/lib/libost_seq_alg.so.2.6.1 ../../stage/lib/libost_conop.so.2.6.1 ../../stage/lib/libost_db.so.2.6.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../stage/lib/libost_seq.so.2.6.1 ../../stage/lib/libost_mol.so.2.6.1 ../../stage/lib/libost_img_alg.so.2.6.1 ../../stage/lib/libost_img.so.2.6.1 ../../stage/lib/libost_info.so.2.6.1 ../../stage/lib/libost_base.so.2.6.1 ../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 /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.1.83.0 /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/current_selection_node.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_argand.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/context_menu.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/custom_part_node.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_manager_gui.cpp make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_part_node.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Built target molck [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_null_overlay.cpp [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_base.cpp In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_node.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/thin_splitter.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/thin_splitter.cc [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/perspective.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/perspective.cc [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_registry.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/widget_registry.cc [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_browser.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/file_browser.cc [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/file_type_dialog.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/scene_win.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/file_viewer.cc.o In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/file_viewer.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/scene_win_model.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/main.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/main.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_modes_node.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/gl_canvas.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/gl_canvas.cc [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/dock_widget.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/dock_widget.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/argand.hh:30, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/main_window.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/main_window.cc [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/gl_win.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/widget.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_menu.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/admin.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/admin.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_pool.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/widget_pool.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/messages/message_widget.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/info_panel.hh:30, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/messages/message_box_widget.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/messages/message_box_widget.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/log_reader.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/messages/log_reader.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data_observer.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/fft_panel.hh:30, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/pointlist_overlay_base.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/sequence_viewer/align_properties_painter.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/align_properties_painter.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/base_row.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/sequence_viewer/background_painter.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/background_painter.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/secstr_row.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/conservation_painter.cc [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/seq_secstr_painter.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/seq_selection_painter.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/seq_selection_painter.cc [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/seq_text_painter.cc [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_delegate.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/measure_tool.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp:10: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/sequence_model.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_model.cc [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_row.cc [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_search_bar.cc [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_table_view.cc [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_viewer.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/file_type_dialog.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/file_type_dialog.cc:19: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/file_type_dialog.hh:26: /usr/include/c++/13/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/tick_painter.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/tick_painter.cc [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/title_row.cc [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/alignment_view_object.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/base_view_object.cc [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_view_object.cc [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main_area.cc.o [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gosty_app.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/main_area.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/gosty_app.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_browser.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/perspective.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/platform.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/perspective.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_state_saver.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/widget_state_saver.cc [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_selection.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_selection.cc.o -MF CMakeFiles/ost_gui.dir/scene_selection.cc.o.d -o CMakeFiles/ost_gui.dir/scene_selection.cc.o -c /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_selection.cc [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/widget_geom_handler.cc [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_loader.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/file_loader.cc [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_bar.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/button_bar.cc [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/drop_box.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/drop_box.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/align_properties_painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/align_properties_painter.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/base_row.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/base_row.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/background_painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/background_painter.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/panel_bar.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/conservation_painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/conservation_painter.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/bottom_bar.cc [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_box.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/button_box.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/seq_secstr_painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/seq_secstr_painter.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/seq_selection_painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/seq_selection_painter.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_search_bar.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_table_view.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_table_view.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_table_view.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/seq_text_painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/seq_text_painter.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/event_button.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/event_button.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_delegate.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/secstr_row.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/base_row.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/base_view_object.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/base_view_object.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/base_row.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/title_row.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_model.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_row.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/title_row.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/panel_manager.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/secstr_row.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/panel_widget_container.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_row.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_view_object.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_row.cc:31: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/panel_bar_widget_holder.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_view_object.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/alignment_view_object.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/alignment_view_object.cc:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /usr/include/boost/ptr_container/ptr_vector.hpp:19, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/side_bar.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/side_bar.cc [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/splitter_panel_bar.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/splitter_panel_bar.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_model.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_model.cc:30: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_model.hh:33: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/file_browser.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/file_browser.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/tabbed_panel_bar.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/gl_canvas.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/glwin_base.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/gl_canvas.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/gl_canvas.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_option_group.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/main.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/main.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/tools/tool_options.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_options.cc [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option.cc.o In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_view_object.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_view_object.cc:32: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_option.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_op.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_menu.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_menu.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/file_browser.cc:34: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_view_object.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/alignment_view_object.hh:32, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/alignment_view_object.cc:41: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_view_object.hh:32: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:30: /build/reproducible-path/openstructure-2.6.1/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++/13/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/tools/tool_manager.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_manager.cc /build/reproducible-path/openstructure-2.6.1/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(QWidget*)': /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(const QString&, QWidget*)': /build/reproducible-path/openstructure-2.6.1/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); | ^~~~~~~~~ [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_options_win.cc [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/gl_win.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/gl_win.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh: In instantiation of 'ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]': /build/reproducible-path/openstructure-2.6.1/modules/gui/src/main.cc:70:69: required from here /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/tick_painter.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/tick_painter.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/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/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/tick_painter.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/tools/mouse_event.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/mouse_event.cc /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/gui/src/main.cc:70:69: required from here /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/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 | ^~~~~~~~~~~~~~~~~~~~~~ [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/manipulator.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/manipulator.cc [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_options_widget.cc [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_bar.cc [ 81%] Linking CXX shared library ../../../../stage/lib/libost_mol_mm.so cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/AMBER03.dat /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/forcefields/AMBER03.dat cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/src/CHARMM27.dat /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/share/openstructure/forcefields/CHARMM27.dat cd /build/reproducible-path/openstructure-2.6.1/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 [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/selection_tool.cc /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol_mm.so.2.6 -o ../../../../stage/lib/libost_mol_mm.so.2.6.1 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../../../../stage/lib/libost_conop.so.2.6.1 ../../../../stage/lib/libost_db.so.2.6.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_seq_alg.so.2.6.1 ../../../../stage/lib/libost_seq.so.2.6.1 ../../../../stage/lib/libost_mol.so.2.6.1 ../../../../stage/lib/libost_img_alg.so.2.6.1 ../../../../stage/lib/libost_img.so.2.6.1 ../../../../stage/lib/libost_info.so.2.6.1 ../../../../stage/lib/libost_base.so.2.6.1 ../../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 /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.1.83.0 /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/measure_tool.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/main_thread_runner.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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/build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/output_redirector.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 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-DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 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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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/path_completer.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_context_parser.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_completer.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_interpreter.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/python_shell/python_interpreter_worker.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_interpreter_worker.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_namespace_tree_model.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_namespace_tree_item.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol_mm.so.2.6.1 ../../../../stage/lib/libost_mol_mm.so.2.6 ../../../../stage/lib/libost_mol_mm.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 83%] Built target ost_mol_mm [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_shell.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_tokenizer.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_shell_text_document_layout.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_shell_widget.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/python_syntax_highlighter.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/shell_history.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_model.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:39: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_op.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_selection.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_selection.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/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/python_shell/string_literal_positions.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/string_literal_positions.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/text_logger.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/state_machine.cc In file included from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_selection.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_selection.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/state.cc /build/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/dir_model.cc: In constructor 'ost::gui::OstDirModel::OstDirModel(QObject*)': /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/dir_model.hh:26, from /build/reproducible-path/openstructure-2.6.1/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); | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/gosty_app.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/gosty_app.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition.cc.o /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/transition.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/drop_box.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/panel_bar.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/panels/panel_bar.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/gosty_app.cc:29: /build/reproducible-path/openstructure-2.6.1/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++/13/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/transition_guard.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/python_shell/transition_guard.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/context_menu.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/current_selection_node.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/custom_part_node.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:31: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:32: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/file_loader.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/file_loader.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/file_loader.cc:19: /usr/include/c++/13/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/scene_win/scene_node.cc.o /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/scene_node.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/label_node.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/entity_node.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/entity_part_node.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/gfx_scene_node.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/file_loader.hh:30: /build/reproducible-path/openstructure-2.6.1/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++/13/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/scene_win/render_mode_node.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/render_mode_node.cc [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/render_modes_node.cc [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/root_node.cc [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/scene_win.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/measure_tool.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/measure_tool.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/measure_tool.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/scene_win_model.cc [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/map_tool.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/map_tool.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/selection_tool.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/selection_tool.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/selection_tool.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 86%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/seq/_ost_seq.so cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.6.1 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.6.1 ../../../../stage/lib/libost_info.so.2.6.1 ../../../../stage/lib/libost_base.so.2.6.1 ../../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/argand.cc [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer.cc [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel.cc [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.6.1/modules/seq/base/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/./__init__.pyc\",\"__init__.py\",doraise=True)" [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/draw_overlay.cc make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 86%] Built target _ost_seq [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/drawing_functions.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/entity_part_node.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/entity_part_node.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 86%] Building CXX object modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_bindings_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/export_tmalign.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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/db/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/pymod/CMakeFiles/_ost_db.dir/DependInfo.cmake "--color=" [ 86%] Building CXX object modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_bindings_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/wrap_bindings.cc 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 [ 86%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/export_linear_db.cc.o make[3]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_db_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/db/pymod/export_linear_db.cc [ 86%] Building CXX object modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/seq/alg/pymod/wrap_seq_alg.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/custom_part_node.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/custom_part_node.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/fft_panel.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/label_node.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/label_node.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/label_node.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/info_panel.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/argand.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/argand.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/argand.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/render_mode_node.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/context_menu.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/pointer_cast.hpp:52, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/context_menu.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/gfx_scene_node.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node_fw.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/gfx_scene_node.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/gfx_scene_node.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/render_mode_node.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/manipulator.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/manipulator.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/scene_win_model.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/scene_win_model.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/scene_win_model.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/drawing_functions.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/drawing_functions.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/drawing_functions.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel.cc:20: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 87%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_db_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/db/pymod/wrap_db.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/draw_overlay.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/entity_part_node.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/custom_part_node.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/img2qt.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/root_node.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/root_node.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/root_node.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, 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:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_bar.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/tool_bar.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/mask_overlay.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/null_overlay.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/overlay_base.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/overlay_manager.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/info_panel.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /usr/include/boost/format.hpp:17, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/info_panel.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/overlay_manager_gui.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_iso.hh:33, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/context_menu.cc:31: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/entity_node.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/context_menu.cc:34: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/pointlist_overlay.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/pointlist_overlay_base.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/scene_win_model.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/strategies.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/viewer_normalizer.cc In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/fft_panel.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/img2qt.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_slab.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/map_tool.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/module_config.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/platform.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/tools/map_tool.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/circle_mask.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/mask_visitor.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/mask_overlay.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/strategies.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/strategies.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/current_selection_node.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/current_selection_node.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/entity_node.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/entity_node.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/viewer_normalizer.cc:30: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/viewer_normalizer.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/pointlist_overlay.cc:28: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/pointlist_overlay.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/pointlist_overlay_base.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/render_modes_node.cc:23: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/render_modes_node.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/render_modes_node.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/overlay_manager.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/overlay_manager.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/bindings/wrap_tmalign.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/export_tmalign.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/bindings/pymod/export_tmalign.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer.cc:36: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/data_viewer/data_viewer.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/db/pymod/export_linear_db.cc:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/db/pymod/export_linear_db.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_selection.hh:23, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/scene_win.cc:25: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/scene_win.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:27: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/modules/gui/src/scene_win/scene_win.cc: In member function 'void ost::gui::SceneWin::RowsInserted(const QModelIndex&, int, int)': /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:34, from /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/merge_pairwise_alignments.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/pymod/wrap_seq_alg.cc:22: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/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, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/pymod/wrap_seq_alg.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/ins_del.hh:25, from /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/pymod/wrap_seq_alg.cc:25: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] Built target ost_img_alg_tests make -f modules/base/tests/CMakeFiles/test_stutil.py_run.dir/build.make modules/base/tests/CMakeFiles/test_stutil.py_run.dir/depend Compound library not available. Some functionality may not work as expected. make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/base/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/test_stutil.py_run.dir/DependInfo.cmake "--color=" [ 95%] Linking CXX executable ../../../../tests/ost_seq_tests cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../../stage/lib/libost_seq.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.6.1 ../../../../stage/lib/libost_info.so.2.6.1 ../../../../stage/lib/libost_base.so.2.6.1 ../../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] running checks test_stutil.py cd /build/reproducible-path/openstructure-2.6.1/modules/base/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/base/tests/test_stutil.py" In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests/test_interaction.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, 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/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests/test_interaction.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ . ---------------------------------------------------------------------- Ran 1 test in 0.089s OK make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] Built target test_aaindex.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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' Compound library not available. Some functionality may not work as expected. cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/base/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/test_table.py_run.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] running checks test_table.py cd /build/reproducible-path/openstructure-2.6.1/modules/base/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/base/tests/test_table.py" ...... ---------------------------------------------------------------------- Ran 6 tests in 0.001s OK make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] Built target test_stutil.py_run 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/base/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/base/tests/CMakeFiles/test_log.py_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 Compound library not available. Some functionality may not work as expected. make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/tests/test_io_sdf.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ [ 95%] running checks test_log.py In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, 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/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.6.1/modules/io/tests/test_io_sdf.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.6.1/modules/base/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/base/tests/test_log.py" /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests/test_block.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, 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/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests/test_block.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make -f modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/depend /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] running checks test_msms.py cd /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests/test_msms.py" Compound library not available. Some functionality may not work as expected. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] Built target ost_seq_tests 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/DependInfo.cmake "--color=" .... ---------------------------------------------------------------------- Ran 4 tests in 0.001s OK In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests/test_block_modifiers.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, 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/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests/test_block_modifiers.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' Compound library not available. Some functionality may not work as expected. [ 95%] running checks test_clustalw.py cd /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests/test_clustalw.py" [ 95%] Built target test_log.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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/DependInfo.cmake "--color=" make -f modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/depend In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/tests/test_mmcif_reader.cc:26: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, 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/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.6.1/modules/io/tests/test_mmcif_reader.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] running checks test_hhblits.py cd /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests/test_hhblits.py" [ 95%] running checks test_blast.py cd /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests/test_blast.py" /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests/test_blast.py:81: SyntaxWarning: invalid escape sequence '\d' re_v = re.compile('\d+\.\d+\.\d+') Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.6.1/modules/io/tests/test_star_parser.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, 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/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.6.1/modules/io/tests/test_star_parser.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ Compound library not available. Some functionality may not work as expected. Could not find msms executable: ignoring unit tests 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/load_map.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/tests/test_exceptions.cc:27: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, 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/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.6.1/modules/io/tests/test_exceptions.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/img/load_map.hh:24, from /build/reproducible-path/openstructure-2.6.1/modules/io/tests/test_io_img.cc:29: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, 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/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.6.1/modules/io/tests/test_io_img.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] Built target test_msms.py_run No HHblits installation found: skip unit tests 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/DependInfo.cmake "--color=" [ 95%] running checks test_kclust.py cd /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests/test_kclust.py" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] Built target test_hhblits.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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] running checks test_naccess.py cd /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests/test_naccess.py" [ 95%] running checks test_cadscore.py cd /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests/test_cadscore.py" Could not find blast executable: ignoring unit tests Compound library not available. Some functionality may not work as expected. .make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] Built target test_blast.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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests/test_forcefield.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, 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/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests/test_forcefield.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] running checks test_tmtools.py cd /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests/test_tmtools.py" Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. .......................Compound library not available. Some functionality may not work as expected. 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] running checks test_ialign.py cd /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests/test_ialign.py" Compound library not available. Some functionality may not work as expected. Could not find kClust executable: ignoring unit tests sCould not find NACCESS, could not test binding... In file included from /usr/include/c++/13/string:54: 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++/13/bits/basic_string.h:899:15, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/13/bits/basic_string.h:1079:16: 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] 1079 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.6.1/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++/13/string:42: 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++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); | ^~~~ make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] Built target test_naccess.py_run In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests/test_topology.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, 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/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests/test_topology.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' .make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 [ 95%] Built target test_kclust.py_run make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/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/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/DependInfo.cmake "--color=" .[ 95%] running checks test_lga.py cd /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests/test_lga.py" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' . ---------------------------------------------------------------------- Ran 1 test in 0.032s OK Could not find ialign master perl script: ignoring unit tests [ 95%] running checks test_hbplus.py cd /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests/test_hbplus.py" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] Built target test_ialign.py_run make -f modules/bindings/tests/CMakeFiles/test_dockq.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_dockq.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/bindings/tests/CMakeFiles/test_dockq.py_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_dockq.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_dockq.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 95%] running checks test_dockq.py cd /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/bindings/tests/test_dockq.py" Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. .Compound library not available. Some functionality may not work as expected. In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, from /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests/test_simulation.cc:21: /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, 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/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests/test_simulation.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ ...............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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' ---------------------------------------------------------------------- cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/conop/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/tests/CMakeFiles/test_processor.py_run.dir/DependInfo.cmake "--color=" Ran 3 tests in 0.408s OK Could not find tmalign executable: ignoring unit tests Could not find tmalign executable: ignoring unit tests make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' .[ 96%] running checks test_processor.py cd /build/reproducible-path/openstructure-2.6.1/modules/conop/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/conop/tests/test_processor.py" Could not find DockQ.py, could not test binding... [ 96%] Built target test_tmtools.py_run make -f modules/conop/tests/CMakeFiles/test_complib.py_run.dir/build.make modules/conop/tests/CMakeFiles/test_complib.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/conop/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/conop/tests/CMakeFiles/test_complib.py_run.dir/DependInfo.cmake "--color=" Could not find hbplus, could not test binding... 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]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/db/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/DependInfo.cmake "--color=" 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/geom/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/geom/tests/CMakeFiles/test_geom.py_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/conop/tests/CMakeFiles/test_complib.py_run.dir/build.make modules/conop/tests/CMakeFiles/test_complib.py_run.dir/build make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 96%] Built target test_dockq.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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/gfx/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 /usr/lib/python3.12/unittest/case.py:589: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/openstructure-2.6.1/modules/base/tests/testfiles/enrichment-out.png'> if method() is not None: ResourceWarning: Enable tracemalloc to get the object allocation traceback ..make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 96%] running checks test_complib.py cd /build/reproducible-path/openstructure-2.6.1/modules/conop/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/conop/tests/test_complib.py" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 96%] running checks test_linear_db.py make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 [ 97%] running checks test_geom.py cd /build/reproducible-path/openstructure-2.6.1/modules/db/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/db/tests/test_linear_db.py" cd /build/reproducible-path/openstructure-2.6.1/modules/geom/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/geom/tests/test_geom.py" make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' Compound library not available. Some functionality may not work as expected. [ 97%] Built target test_hbplus.py_run 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/img/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 [ 97%] running checks test_gfx.py cd /build/reproducible-path/openstructure-2.6.1/modules/gfx/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/gfx/tests/test_gfx.py" make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' .. ---------------------------------------------------------------------- Ran 1 test in 0.044s OK Could not find lga executable: ignoring unit tests [ 97%] running checks for module img_alg cd /build/reproducible-path/openstructure-2.6.1/modules/img/alg/tests && env OST_ROOT=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/tests/ost_img_alg_tests .. ---------------------------------------------------------------------- Ran 1 test in 0.001s OK Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/io/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/DependInfo.cmake "--color=" Compound library not available. Some functionality may not work as expected. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' . ---------------------------------------------------------------------- Ran 7 tests in 1.476s OK Compound library not available. Some functionality may not work as expected. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 97%] Built target test_lga.py_run Running 25 test cases... *** No errors detected 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]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/io/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/DependInfo.cmake "--color=" [ 97%] running checks test_io_pdb.py cd /build/reproducible-path/openstructure-2.6.1/modules/io/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/io/tests/test_io_pdb.py" [ 97%] Built target ost_img_alg_tests_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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/io/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 . ---------------------------------------------------------------------- Ran 3 tests in 0.004s OK make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' ........ ---------------------------------------------------------------------- Ran 8 tests in 0.004s OK make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 97%] running checks test_io_mmcif.py make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/modules/io/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/io/tests/test_io_mmcif.py" [ 97%] running checks test_io_omf.py cd /build/reproducible-path/openstructure-2.6.1/modules/io/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/io/tests/test_io_omf.py" [ 97%] Built target test_clustalw.py_run make -f modules/io/tests/CMakeFiles/test_io_sdf.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_sdf.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/io/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_io_sdf.py_run.dir/DependInfo.cmake "--color=" [ 97%] Built target test_linear_db.py_run make -f modules/mol/base/tests/CMakeFiles/test_invalid.py_run.dir/build.make modules/mol/base/tests/CMakeFiles/test_invalid.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/base/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/base/tests/CMakeFiles/test_invalid.py_run.dir/DependInfo.cmake "--color=" 0..h.... ---------------------------------------------------------------------- Ran 6 tests in 0.003s OK NOmake[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/io/tests/CMakeFiles/test_io_sdf.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_sdf.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/mol/base/tests/CMakeFiles/test_invalid.py_run.dir/build.make modules/mol/base/tests/CMakeFiles/test_invalid.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 98%] running checks test_io_sdf.py Compound library not available. Some functionality may not work as expected. cd /build/reproducible-path/openstructure-2.6.1/modules/io/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/io/tests/test_io_sdf.py" [ 98%] running checks test_invalid.py 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_pdbize.py_run.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/openstructure-2.6.1/modules/mol/base/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/mol/base/tests/test_invalid.py" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 98%] Built target test_gfx.py_run make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/depend 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_convenient_superpose.py_run.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' Compound library not available. Some functionality may not work as expected. [ 98%] running checks test_pdbize.py Compound library not available. Some functionality may not work as expected. cd /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests/test_pdbize.py" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [ 98%] Built target test_processor.py_run [ 98%] Built target test_geom.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 -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_accessibility.py_run.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_hbond.py_run.dir/DependInfo.cmake "--color=" [ 98%] running checks test_convenient_superpose.py cd /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests/test_convenient_superpose.py" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. [100%] running checks test_accessibility.py [100%] running checks test_hbond.py cd /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests/test_accessibility.py" cd /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests/test_hbond.py" Compound library not available. Some functionality may not work as expected. .Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. ....... ---------------------------------------------------------------------- Ran 7 tests in 0.002s OK No compound library available. Ignoring test_stereochemistry.py tests. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target test_invalid.py_run 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/depend make -f modules/mol/alg/tests/CMakeFiles/test_lddt.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_lddt.py_run.dir/depend In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37, from /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests/test_topology.cc:22: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_sec_struct.py_run.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_lddt.py_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' ....s ---------------------------------------------------------------------- Ran 5 tests in 0.005s OK (skipped=1) make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 -f modules/mol/alg/tests/CMakeFiles/test_lddt.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_lddt.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target test_io_omf.py_run make -f modules/mol/alg/tests/CMakeFiles/test_qsscore.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_qsscore.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_qsscore.py_run.dir/DependInfo.cmake "--color=" [100%] running checks test_sec_struct.py [100%] running checks test_lddt.py cd /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests/test_lddt.py" cd /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests/test_sec_struct.py" ........ ---------------------------------------------------------------------- Ran 8 tests in 0.009s OK make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target test_io_pdb.py_run make -f modules/mol/alg/tests/CMakeFiles/test_stereochemistry.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_stereochemistry.py_run.dir/depend [100%] Built target test_pdbize.py_run make -f modules/mol/alg/tests/CMakeFiles/test_contact_score.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_contact_score.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_contact_score.py_run.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_stereochemistry.py_run.dir/DependInfo.cmake "--color=" SEQRES import requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. SEQRES import requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' .No citation for identifier '1' found. Couldn't set author list. ..SEQRES import requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. ... ---------------------------------------------------------------------- Ran 4 tests in 0.035s OK make -f modules/mol/alg/tests/CMakeFiles/test_qsscore.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_qsscore.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' .Compound library not available. Some functionality may not work as expected. . ---------------------------------------------------------------------- Ran 2 tests in 0.015s OK make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/mol/alg/tests/CMakeFiles/test_contact_score.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_contact_score.py_run.dir/build make -f modules/mol/alg/tests/CMakeFiles/test_stereochemistry.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_stereochemistry.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] running checks test_qsscore.py cd /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests/test_qsscore.py" /usr/lib/python3.12/unittest/case.py:589: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/openstructure-2.6.1/modules/base/tests/testfiles/roc-out.png'> if method() is not None: ResourceWarning: Enable tracemalloc to get the object allocation traceback .[100%] running checks test_contact_score.py [100%] running checks test_stereochemistry.py cd /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests/test_stereochemistry.py" cd /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests/test_contact_score.py" .make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' Compound library not available. Some functionality may not work as expected. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target test_hbond.py_run make -f modules/mol/alg/tests/CMakeFiles/test_biounit.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_biounit.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/alg/tests/CMakeFiles/test_biounit.py_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make -f modules/mol/alg/tests/CMakeFiles/test_biounit.py_run.dir/build.make modules/mol/alg/tests/CMakeFiles/test_biounit.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' Compound library not available. Some functionality may not work as expected. [100%] running checks test_biounit.py cd /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/mol/alg/tests/test_biounit.py" Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. In file included from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests/test_simulation.cc:29: /build/reproducible-path/openstructure-2.6.1/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++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ Compound library not available. Some functionality may not work as expected. [100%] Built target test_io_sdf.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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/mol/mm/tests/CMakeFiles/test_antechamber.py_run.dir/DependInfo.cmake "--color=" ss ---------------------------------------------------------------------- Ran 1 test in 0.000s OK (skipped=1) make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Linking CXX executable ../../../../tests/ost_mol_alg_tests cd /build/reproducible-path/openstructure-2.6.1/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 [100%] running checks test_antechamber.py cd /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/mol/mm/tests/test_antechamber.py" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../../stage/lib/libost_io.so.2.6.1 ../../../../stage/lib/libost_mol_alg.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_seq_alg.so.2.6.1 ../../../../stage/lib/libost_img_alg.so.2.6.1 ../../../../stage/lib/libost_img.so.2.6.1 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_conop.so.2.6.1 ../../../../stage/lib/libost_db.so.2.6.1 ../../../../stage/lib/libost_seq.so.2.6.1 ../../../../stage/lib/libost_mol.so.2.6.1 ../../../../stage/lib/libost_info.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../../stage/lib/libost_base.so.2.6.1 ../../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' /usr/lib/python3.12/unittest/case.py:589: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/openstructure-2.6.1/modules/base/tests/testfiles/roc-same-val-out.png'> if method() is not None: ResourceWarning: Enable tracemalloc to get the object allocation traceback ........../build/reproducible-path/openstructure-2.6.1/modules/conop/tests/test_complib.py:65: UserWarning: Compound library not available. Some functionality may not work as expected. warnings.warn("Compound library not available. Some functionality may not work as expected.") .... ---------------------------------------------------------------------- Ran 5 tests in 0.768s OK .SEQRES import requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. unknown residue 'ACE' in SEQRES record. Setting one-letter-code to 'X' ....[100%] Built target test_sec_struct.py_run .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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/seq/base/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/DependInfo.cmake "--color=" E........................ ====================================================================== ERROR: testSpearmanCorrel (__main__.TestTable.testSpearmanCorrel) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/openstructure-2.6.1/modules/base/tests/test_table.py", line 1668, in testSpearmanCorrel self.assertAlmostEqual(tab.SpearmanCorrel('second','third'), -0.316227766) File "/usr/lib/python3.12/unittest/case.py", line 916, in assertAlmostEqual diff = abs(first - second) ~~~~~~^~~~~~~~ TypeError: unsupported operand type(s) for -: 'NoneType' and 'float' ---------------------------------------------------------------------- Ran 83 tests in 2.136s FAILED (errors=1) No compound library available. Ignoring test_stereochemistry.py tests. Compound library not available. Some functionality may not work as expected. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] running checks for module seq [100%] Built target test_complib.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 cd /build/reproducible-path/openstructure-2.6.1/modules/seq/base/tests && env OST_ROOT=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/tests/ost_seq_tests make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/seq/base/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/base/tests/CMakeFiles/test_seq.py_run.dir/DependInfo.cmake "--color=" 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]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_renumber.py_run.dir/DependInfo.cmake "--color=" 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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_local_align.py_run.dir/DependInfo.cmake "--color=" Running 32 test cases... *** No errors detected make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target test_stereochemistry.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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_global_align.py_run.dir/DependInfo.cmake "--color=" [100%] Built target ost_seq_tests_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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_semiglobal_align.py_run.dir/DependInfo.cmake "--color=" .[100%] running checks test_seq.py [100%] running checks test_renumber.py cd /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests/test_renumber.py" cd /build/reproducible-path/openstructure-2.6.1/modules/seq/base/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/seq/base/tests/test_seq.py" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' . ---------------------------------------------------------------------- Ran 1 test in 0.222s OK [100%] running checks test_local_align.py make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 cd /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests/test_local_align.py" make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] running checks test_global_align.py cd /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests/test_global_align.py" .[100%] running checks test_semiglobal_align.py No compound library available. Ignoring test_lddt.py tests. cd /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests/test_semiglobal_align.py" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' .No compound lib available. Ignoring test_qsscore.py tests. . ---------------------------------------------------------------------- Ran 3 tests in 0.034s OK Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. [100%] Built target test_biounit.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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_weight_matrix.py_run.dir/DependInfo.cmake "--color=" No compound lib available. Ignoring contact_score.py tests. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target test_antechamber.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]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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 Compound library not available. Some functionality may not work as expected. make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.6.1 /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/tests /build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_alignment_from_chain_view.py_run.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' Compound library not available. Some functionality may not work as expected. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' Compound library not available. Some functionality may not work as expected. [100%] running checks test_weight_matrix.py make[4]: *** [modules/base/tests/CMakeFiles/test_table.py_run.dir/build.make:74: modules/base/tests/CMakeFiles/test_table.py_run] Error 1 make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests/test_weight_matrix.py" make[3]: *** [CMakeFiles/Makefile2:2100: modules/base/tests/CMakeFiles/test_table.py_run.dir/all] Error 2 make[3]: *** Waiting for unfinished jobs.... [100%] running checks test_alignment_from_chain_view.py [100%] Built target test_lddt.py_run cd /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.6.1/modules/seq/alg/tests/test_alignment_from_chain_view.py" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' .[100%] Built target test_qsscore.py_run make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target test_contact_score.py_run Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. .............. ---------------------------------------------------------------------- Ran 14 tests in 0.008s OK make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' ..[100%] Built target ost_mol_alg_tests .make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' ....[100%] Built target test_seq.py_run . ---------------------------------------------------------------------- Ran 8 tests in 0.052s OK .... ---------------------------------------------------------------------- Ran 3 tests in 0.002s SEQRES import requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' OK unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' .... ---------------------------------------------------------------------- Ran 3 tests in 0.002s OK .. ---------------------------------------------------------------------- Ran 1 test in 0.003s OK ---------------------------------------------------------------------- Ran 1 test in 0.001s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.000s OK make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target test_renumber.py_run [100%] Built target test_alignment_from_chain_view.py_run make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target test_local_align.py_run .make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target test_global_align.py_run [100%] Built target test_semiglobal_align.py_run make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target test_weight_matrix.py_run ...SEQRES import requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. ......s ---------------------------------------------------------------------- Ran 11 tests in 1.555s OK (skipped=1) .. ---------------------------------------------------------------------- Ran 9 tests in 1.585s OK make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target test_io_mmcif.py_run make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target test_convenient_superpose.py_run [100%] Linking CXX executable ../../../tests/ost_gfx_tests cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../stage/lib/libost_gfx.so.2.6.1 ../../../stage/lib/libost_io.so.2.6.1 /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.2.6.1 ../../../stage/lib/libost_conop.so.2.6.1 ../../../stage/lib/libost_db.so.2.6.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.6.1 ../../../stage/lib/libost_img.so.2.6.1 /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.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_seq_alg.so.2.6.1 ../../../stage/lib/libost_seq.so.2.6.1 ../../../stage/lib/libost_mol.so.2.6.1 ../../../stage/lib/libost_info.so.2.6.1 ../../../stage/lib/libost_base.so.2.6.1 ../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target ost_gfx_tests [100%] Linking CXX executable ../../../../tests/ost_mol_tests cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.6.1 ../../../../stage/lib/libost_info.so.2.6.1 ../../../../stage/lib/libost_base.so.2.6.1 ../../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 . ---------------------------------------------------------------------- Ran 2 tests in 2.792s OK (skipped=1) Could not find NACCESS, could not compare Accessiblity function... make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target test_accessibility.py_run make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target ost_mol_tests [100%] Linking CXX executable ../../../../tests/ost_seq_alg_tests cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../../stage/lib/libost_io.so.2.6.1 ../../../../stage/lib/libost_mol_alg.so.2.6.1 ../../../../stage/lib/libost_seq_alg.so.2.6.1 ../../../../stage/lib/libost_conop.so.2.6.1 ../../../../stage/lib/libost_db.so.2.6.1 ../../../../stage/lib/libost_seq.so.2.6.1 ../../../../stage/lib/libost_mol.so.2.6.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_img_alg.so.2.6.1 ../../../../stage/lib/libost_img.so.2.6.1 ../../../../stage/lib/libost_info.so.2.6.1 ../../../../stage/lib/libost_base.so.2.6.1 ../../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 /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.1.83.0 /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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target ost_seq_alg_tests [100%] Linking CXX executable ../../../tests/ost_conop_tests cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../stage/lib/libost_conop.so.2.6.1 ../../../stage/lib/libost_db.so.2.6.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.6.1 ../../../stage/lib/libost_mol.so.2.6.1 ../../../stage/lib/libost_info.so.2.6.1 ../../../stage/lib/libost_base.so.2.6.1 ../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target ost_conop_tests [100%] Linking CXX executable ../../../../tests/ost_mol_mm_tests cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../../stage/lib/libost_mol_mm.so.2.6.1 ../../../../stage/lib/libost_io.so.2.6.1 ../../../../stage/lib/libost_mol_alg.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 ../../../../stage/lib/libost_conop.so.2.6.1 ../../../../stage/lib/libost_db.so.2.6.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_seq_alg.so.2.6.1 ../../../../stage/lib/libost_seq.so.2.6.1 ../../../../stage/lib/libost_mol.so.2.6.1 ../../../../stage/lib/libost_img_alg.so.2.6.1 ../../../../stage/lib/libost_img.so.2.6.1 ../../../../stage/lib/libost_info.so.2.6.1 ../../../../stage/lib/libost_base.so.2.6.1 ../../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 /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.1.83.0 /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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target ost_mol_mm_tests . ---------------------------------------------------------------------- Ran 2 tests in 14.461s OK (skipped=1) make[4]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target test_cadscore.py_run [100%] Linking CXX executable ../../../tests/ost_io_tests cd /build/reproducible-path/openstructure-2.6.1/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/reproducible-path/openstructure-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_sdf_v3000.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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../stage/lib/libost_io.so.2.6.1 ../../../stage/lib/libost_mol_alg.so.2.6.1 ../../../stage/lib/libost_conop.so.2.6.1 ../../../stage/lib/libost_db.so.2.6.1 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_seq_alg.so.2.6.1 ../../../stage/lib/libost_seq.so.2.6.1 ../../../stage/lib/libost_mol.so.2.6.1 ../../../stage/lib/libost_img_alg.so.2.6.1 ../../../stage/lib/libost_img.so.2.6.1 ../../../stage/lib/libost_info.so.2.6.1 ../../../stage/lib/libost_base.so.2.6.1 ../../../stage/lib/libost_geom.so.2.6.1 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 /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.1.83.0 /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/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' [100%] Built target ost_io_tests make[3]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[2]: *** [CMakeFiles/Makefile2:1704: CMakeFiles/check.dir/rule] Error 2 make[2]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' make[1]: *** [Makefile:192: check] Error 2 make[1]: Leaving directory '/build/reproducible-path/openstructure-2.6.1/obj-x86_64-linux-gnu' dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j42 check ARGS\+=--verbose ARGS\+=-j42 returned exit code 2 make: *** [debian/rules:11: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/2221909 and its subdirectories