Diff of the two buildlogs: -- --- b1/build.log 2024-06-03 18:04:09.404059752 +0000 +++ b2/build.log 2024-06-03 17:35:51.512136943 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 3 05:35:58 -12 2024 -I: pbuilder-time-stamp: 1717436158 +I: Current time: Mon Jul 7 13:48:14 +14 2025 +I: pbuilder-time-stamp: 1751845694 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -33,52 +33,84 @@ 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/3896421/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1305528/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 6 23:48 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1305528/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1305528/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=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='424cfc4f17e946b98aa7494a3b85f021' - 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='3896421' - PS1='# ' - PS2='> ' + INVOCATION_ID=5562868e775a4975a4289d553fe33c65 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1305528 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.iLgAMUSR/pbuilderrc_vxpx --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.iLgAMUSR/b1 --logfile b1/build.log openstructure_2.5.0-2.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.iLgAMUSR/pbuilderrc_C68k --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.iLgAMUSR/b2 --logfile b2/build.log openstructure_2.5.0-2.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 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 3 07:43 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3896421/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jul 5 14:05 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1305528/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -599,7 +631,7 @@ Get: 439 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5.sip amd64 12.13.0-1+b1 [79.5 kB] Get: 440 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5 amd64 5.15.10+dfsg-1+b2 [2501 kB] Get: 441 http://deb.debian.org/debian unstable/main amd64 voronota amd64 1.22.3149-2 [2057 kB] -Fetched 300 MB in 16s (18.5 MB/s) +Fetched 300 MB in 22s (13.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19705 files and directories currently installed.) @@ -2001,8 +2033,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Jun 3 17:39:41 UTC 2024. -Universal Time is now: Mon Jun 3 17:39:41 UTC 2024. +Local time is now: Sun Jul 6 23:51:11 UTC 2025. +Universal Time is now: Sun Jul 6 23:51:11 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-3) ... @@ -2400,7 +2432,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/openstructure-2.5.0/ && 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_2.5.0-2_source.changes +I: user script /srv/workspace/pbuilder/1305528/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1305528/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/openstructure-2.5.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../openstructure_2.5.0-2_source.changes dpkg-buildpackage: info: source package openstructure dpkg-buildpackage: info: source version 2.5.0-2 dpkg-buildpackage: info: source distribution unstable @@ -2489,8 +2525,8 @@ Static Libraries (-DENABLE_STATIC) : OFF Debian/Ubuntu directory layout (-DUBUNTU_LAYOUT) : ON Hidden object visibility (-DHIDDEN_VISIBILITY) : OFF --- Configuring done (4.0s) --- Generating done (1.0s) +-- Configuring done (1.8s) +-- Generating done (0.5s) CMake Warning: Manually-specified variables were not used by the project: @@ -2506,7 +2542,7 @@ -- Build files have been written to: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/openstructure-2.5.0' dh_auto_build - cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/openstructure-2.5.0 -B/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -2517,1275 +2553,1275 @@ 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-2.5.0/obj-x86_64-linux-gnu' -make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/depend cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/create_stage.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-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/subst___init__.py.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 -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/subst___init__.py.dir/DependInfo.cmake "--color=" make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/depend -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-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/depend cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/db/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod/CMakeFiles/ost_db_pymod.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 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/DependInfo.cmake "--color=" make -f modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/DependInfo.cmake "--color=" +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-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/share /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share/CMakeFiles/scene_icons.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/DependInfo.cmake "--color=" +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]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/share /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share/CMakeFiles/gui_images.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/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/DependInfo.cmake "--color=" +make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/DependInfo.cmake "--color=" -make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/depend -make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/depend -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 -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/DependInfo.cmake "--color=" +make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/DependInfo.cmake "--color=" +make -f modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build.make modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/info/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/ost_info_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-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/io/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod/CMakeFiles/ost_io_pymod.dir/DependInfo.cmake "--color=" +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-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/DependInfo.cmake "--color=" +make -f modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build.make modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/depend +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-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/info/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/ost_info_pymod.dir/DependInfo.cmake "--color=" -make -f modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build.make modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/depend +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -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 cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/DependInfo.cmake "--color=" -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-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 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actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_startup.py.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_config.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/actions /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions 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/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib +make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build +make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/db/./__init__.py +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./__init__.py +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +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-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.py.dir/build +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/alg/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +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[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./__init__.py -make -f modules/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.py.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/__init__.py.in -DOUT_FILE=__init__.py -DALL_ADDITIONAL_MODULES=,\'gui\',\'gfx\',\'img\',\'info\' -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./__init__.py -make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/geom/./__init__.py -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_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 -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/build make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./__init__.py -make -f modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_dng_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[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/db/./__init__.py -make -f modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build.make modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./__init__.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/add_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/add_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./__init__.py +make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/images/logo-small.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/images/logo-small.png +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]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/__init__.py -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/__init__.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/add_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/add_icon.png +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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 -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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build +make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/./__init__.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/alg/./__init__.py -make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build -make -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[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/./__init__.py +make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/__init__.py 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 make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/info/./__init__.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/scripts/ost_config.in -DOUT_FILE=ost_config -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.9 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake +make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/./__init__.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./__init__.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./__init__.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/info/./__init__.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./__init__.py +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./__init__.py -make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/bin -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./__init__.py -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]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/./__init__.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/tests +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/./__init__.py +make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./views.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./views.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/close_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/close_icon.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/./py_gfx_obj.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./py_gfx_obj.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_context_menu.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_context_menu.py +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/scripts/dng.in -DOUT_FILE=dng -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.9 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake +make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/actions/ost-compare-ligand-structures /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-ligand-structures +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-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/scripts/ost.in -DOUT_FILE=ost -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.9 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/scripts/ost_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.9 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/color_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_options_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/bin +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_context_menu.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_context_menu.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./lga.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./lga.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/./py_gfx_obj.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./py_gfx_obj.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/./cleanup.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./cleanup.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/pymod/./antechamber.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./antechamber.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/termuse.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/termuse.py -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./lga.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./lga.py -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 0%] Built target ost_geom_pymod -[ 0%] Built target gui_images -[ 0%] Built target ost_img_pymod -[ 0%] Built target ost_info_pymod -[ 0%] Built target subst___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 -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/depend -make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/depend -make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/depend -make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_startup.py.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_config.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake "--color=" -[ 0%] Built target ost_mol_pymod -make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/actions /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" -[ 0%] Built target create_stage -[ 0%] Built target ost_seq_pymod -make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/depend -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-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/geom/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom_headers.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/config /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config_headers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/termuse.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/termuse.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./mat.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./mat.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./views.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./views.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/close_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/close_icon.png make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/color_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_options_widget.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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 -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/./remote.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./remote.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/pymod/./antechamber.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./antechamber.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_menubar.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_menubar.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/scripts/ost.in -DOUT_FILE=ost -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.9 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./__init__.py -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/scripts/ost_config.in -DOUT_FILE=ost_config -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.9 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/scripts/dng.in -DOUT_FILE=dng -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.9 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/scripts/ost_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.9 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/actions/ost-compare-structures /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-structures make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 0%] Built target ost_db_pymod -[ 0%] Built target ost_img_alg_pymod -make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./superpose.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./superpose.py -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/actions/ost-compare-ligand-structures /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-ligand-structures -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/superpositiondialog.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/superpositiondialog.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hbplus.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hbplus.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/color_select_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_select_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_menubar.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_menubar.py +[ 0%] Built target gui_images make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/./remote.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./remote.py -make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/ost_base_headers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/critical_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/critical_icon.png +[ 0%] Built target ost_img_alg_pymod +[ 0%] Built target ost_geom_pymod make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./renumber.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./renumber.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hbplus.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hbplus.py +[ 0%] Built target subst___init__.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./superpose.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./superpose.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/superpositiondialog.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/superpositiondialog.py 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-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/export_helper/vector.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/export_helper/vector.hh -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/config/./base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./mat.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./mat.py -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/ost_base_pymod.dir/DependInfo.cmake "--color=" +[ 0%] Built target ost_info_pymod +[ 0%] Built target subst_ost_config +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/critical_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/critical_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/tests +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_spacenav.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_spacenav.py +[ 0%] Built target ost_mol_pymod make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 0%] Built target ost_img_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/color_select_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_select_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/./repository.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./repository.py +[ 0%] Built target ost_seq_pymod +[ 0%] Built target subst_dng +[ 0%] Built target subst_ost_startup.py [ 0%] Built target ost_conop_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/actions/ost-compare-structures-legacy /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-structures-legacy +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./aaindex.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./aaindex.py +[ 0%] Built target subst_ost cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./qsscoring.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./qsscoring.py [ 0%] Built target ost_gfx_pymod -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/actions/ost-compare-structures /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-structures +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/delete_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/delete_icon.png +make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 0%] Built target ost_mol_mm_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_splash.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_splash.py +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./settings.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/combo_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/combo_options_widget.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./msms.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./msms.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_spacenav.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_spacenav.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/combo_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/combo_options_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/./repository.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./repository.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/init.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/init.py -make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/build -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./def.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./def.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./renumber.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./renumber.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/delete_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/delete_icon.png -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/export_helper/generic_property_def.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/export_helper/generic_property_def.hh -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-2.5.0/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/config/./config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./config.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/DependInfo.cmake "--color=" -make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/info/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src/CMakeFiles/ost_info_headers.dir/DependInfo.cmake "--color=" -[ 0%] Built target subst_ost_config -[ 0%] Built target subst_dng +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/aaindex1 /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex1 cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./trajectory_analysis.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./trajectory_analysis.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./tmtools.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./tmtools.py +[ 0%] Built target create_stage +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-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/distance_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/distance_icon.png +make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/depend +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./trajectory_viewer.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./trajectory_viewer.py +make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend +[ 0%] Built target ost_io_pymod +make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/depend +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./stutil.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.py +make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/actions/ost-compare-structures-legacy /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-structures-legacy -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./settings.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.py -[ 0%] Built target subst_ost +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/geom/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom_headers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/cpk_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/cpk_widget.py make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/DependInfo.cmake "--color=" -[ 0%] Built target subst_ost_startup.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/cpk_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/cpk_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/config /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config_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/depend -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/bindings/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_splash.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_splash.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/menu.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/menu.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./exc.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./exc.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./aaindex.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./aaindex.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/ost_base_headers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./tmtools.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./tmtools.py +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/DependInfo.cmake "--color=" make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/info/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_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 +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/menu.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/menu.py +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/bindings/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/DependInfo.cmake "--color=" +make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/conop/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop_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-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/distance_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/distance_icon.png cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/db/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src/CMakeFiles/ost_db_headers.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/config/./dllexport.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./dllexport.hh +make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/depend +make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/DependInfo.cmake "--color=" -make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build +make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./stutil.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/export_helper/pair_to_tuple_conv.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./dssp.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dssp.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake "--color=" +make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/DependInfo.cmake "--color=" +[ 0%] Built target actions +make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/io/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src/CMakeFiles/ost_io_headers.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gfx/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/aaindex2 /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex2 cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./structure_analysis.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./structure_analysis.py -[ 0%] Built target ost_io_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/find_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/find_icon.png +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/custom_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/custom_widget.py +make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu' +make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./trajectory_viewer.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./trajectory_viewer.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/config/./version.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./version.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./geom.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./geom.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/find_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/find_icon.png +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/config/./base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./base.hh +make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build 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-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/pointer_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh -make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/export_helper/generic_property_def.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/export_helper/generic_property_def.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build -make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./helpwidget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./helpwidget.py +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-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./table.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info.hh +make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/./wrap_tmalign.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/bindings/./wrap_tmalign.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/aaindex1 /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex1 +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./conop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./conop.hh -make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./table.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.py -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./clustalw.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./clustalw.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-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/pointer_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./sqlite_wrap.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh -make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/export_helper/vec_to_list_conv.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/export_helper/vec_to_list_conv.hh -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./alignment_opts.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./alignment_opts.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./helix_kinks.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./helix_kinks.py -[ 0%] Built target ost_gui_dng_pymod -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_editor_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_editor_widget.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/information_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/information_icon.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./helpwidget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./helpwidget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_group.hh -make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./table_selector.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_error.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_error.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./processor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./processor.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/DependInfo.cmake "--color=" -[ 0%] Built target actions -make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./utils.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./utils.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./conop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./conop.hh +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-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./dssp.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dssp.py +make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./clip_alignment.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/io/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src/CMakeFiles/ost_io_headers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_info_handler.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/aaindex2 /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex2 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./hbond.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./hbond.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/test_utils/compare_files.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/test_utils/compare_files.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./sqlite_conv.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_conv.hh -[ 0%] Built target ost_config_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/map_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/map_icon.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./table.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./table.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-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_prop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/raster_image/raster_image.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat2.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat2.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./amino_acids.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./amino_acids.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/export_helper/vector.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/export_helper/vector.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/build -[ 0%] Built target ost_bindings_headers -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./conservation.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./conservation.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/chemdict_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./xmlrunner.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.py -make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build +make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build +make -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-2.5.0/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 make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./generic_property.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./generic_property.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./lddt.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./lddt.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/aaindex3 /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex3 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./naccess.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./naccess.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh -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]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gfx/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_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/build -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/./wrap_tmalign.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/bindings/./wrap_tmalign.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./helix_kinks.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./helix_kinks.py +make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/raster_image/raster_image.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./alignment_opts.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./alignment_opts.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./anisotropic.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./anisotropic.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/menubar_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/menubar_icon.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./gosty_startup.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./gosty_startup.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 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat3.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat3.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_list_model.py +make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./svd_superpose.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./svd_superpose.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_handle.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./auto_correlate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/dispatch.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/dispatch.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hhblits.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./integrity_error.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./integrity_error.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/rigid_body_manipulator_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/rigid_body_manipulator_icon.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./linear_indexer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./linear_indexer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./qsscore.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./qsscore.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_preset_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_preset_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./diag.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./diag.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat4.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat4.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/star_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/star_parser.hh -make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./testutils.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.py -[ 0%] Built target ost_gui_pymod -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-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake "--color=" -[ 0%] Built target ost_seq_alg_pymod -make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/chemdict_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./forcefield.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./forcefield.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/information_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/information_icon.png +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/aaindex3 /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex3 +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_editor_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_editor_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/config/./config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_error.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_error.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_group.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/export_helper/pair_to_tuple_conv.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./sqlite_conv.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_conv.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./processor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./processor.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./clustalw.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./clustalw.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./table.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./table.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./table_selector.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.py +[ 0%] Built target ost_gui_dng_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./clip_alignment.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./auto_correlate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/dispatch.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/dispatch.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./def.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./def.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_s.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_info_handler.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./hbond.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./hbond.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_prop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/config/./dllexport.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./dllexport.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./ff_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./ff_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_option_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/map_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/map_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./amino_acids.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./amino_acids.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/star_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/star_parser.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/export_helper/vec_to_list_conv.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/export_helper/vec_to_list_conv.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./conservation.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./conservation.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./utils.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./utils.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./exc.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./exc.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./clear.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clear.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./invalid_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./invalid_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/selection_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/selection_icon.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_group.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/hsc_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/hsc_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./model_check.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./model_check.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different __init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/__init__.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./scoring.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./scoring.py -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./sec_structure_segments.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./forcefield.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./forcefield.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./sequence_list.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_list.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./gosty_startup.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./gosty_startup.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./xmlrunner.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./lddt.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./lddt.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_list_model.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh +[ 0%] Built target ost_bindings_headers cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_s.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hhblits2.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits2.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./buildingblock.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./buildingblock.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/config/./version.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./version.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./sec_structure_segments.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./diag.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./diag.hh +[ 0%] Built target ost_seq_alg_pymod cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./contact_prediction_score.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./binary_container.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./binary_container.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_option_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/show_sidebar_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/show_sidebar_icon.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_info.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./ff_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./ff_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/menubar_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/menubar_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./geom.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./geom.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./linear_indexer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./linear_indexer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/test_utils/compare_files.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/test_utils/compare_files.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./qsscore.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./qsscore.py +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_preset_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_preset_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_spec.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./naccess.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./naccess.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./block_modifiers.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./block_modifiers.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./clip_min_max.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./testutils.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./model_check.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./model_check.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./sequence_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec2.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec2.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hhblits3.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits3.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./chain_mapping.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./chain_mapping.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./contact_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_info.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./binary_container.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./binary_container.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./local_dist_diff_test.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./local_dist_diff_test.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_item.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_item.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./scoring.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./scoring.py +[ 0%] Built target ost_gui_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./generic_property.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./generic_property.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./sequence_list.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_list.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/rigid_body_manipulator_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/rigid_body_manipulator_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_group.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./heuristic.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./heuristic.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./clip_min_max.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./ptr_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./ptr_observer.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/immutable_gradient_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_gradient_info_handler.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_s.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./buildingblock.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./buildingblock.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/site_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/site_icon.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./contact_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./blast.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./blast.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./extract_data_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./extract_data_helper.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./stereochemistry.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./stereochemistry.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./distance_test_common.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/io_profile.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec3.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec3.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hhblits.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/hsc_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/hsc_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different __init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/__init__.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./alignment_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./alignment_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./log.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./log.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./compound.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_spec.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./conjugate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./conjugate.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/split_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/split_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_octree.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./distance_map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./cadscore.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./cadscore.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./distance_rmsd_test.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_rmsd_test.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/immutable_preset_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_preset_info_handler.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_base_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./block_modifiers.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./block_modifiers.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./module_config.hh -[ 0%] Built target ost_base_pymod +[ 0%] Built target ost_config_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./conjugate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./conjugate.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./heuristic.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./heuristic.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/selection_tool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/dcd_io.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./gromacs_block_modifiers.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./gromacs_block_modifiers.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/io_profile.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/config /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./ligand_scoring.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./ligand_scoring.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./log_sink.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./log_sink.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec4.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec4.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_octree.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./distance_test_common.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./chain_mapping.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./chain_mapping.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./extract_data_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./extract_data_helper.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./integrity_error.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./integrity_error.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./sequence_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat2.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat2.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/selection_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/selection_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_item.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_item.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_base_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hhblits2.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits2.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./entropy.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./entropy.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./kclust.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./kclust.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_path.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_path.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./sequence_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./superpose_frames.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./gromacs_block_modifiers.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./gromacs_block_modifiers.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_def.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/warning_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/warning_icon.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/init_inspector.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/init_inspector.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_crd_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./compound_lib.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/selection_tool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./convolute.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./convolute.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/immutable_gradient_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_gradient_info_handler.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./compound.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/measure_tool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/octree_isocont.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./dockq.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./dockq.py -[ 0%] Built target ost_db_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./filter_clashes.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./ialign.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./ialign.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./aligned_region.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_region.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./profile.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./profile.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/dcd_io.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./heuristic_block_modifiers.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./heuristic_block_modifiers.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./global_align.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./global_align.hh make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/inspector_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/inspector_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_set.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_set.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_factory.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_factory.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/refresh.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/refresh.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/measure_tool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pqr_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pqr_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./dyn_cast.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./dyn_cast.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./construct_cbeta.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./mmseqs2.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./mmseqs2.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./aligned_column.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat2_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./correlate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./correlate.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/stereo_data.json /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/stereo_data.json -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cartoon_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/map_level_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/map_level_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/dihedral.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/dihedral.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_visitor.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./clash_score.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat3_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./aligned_column_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./dockq.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dockq.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./cross_correlate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./cross_correlate.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./stereochemistry.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./stereochemistry.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./invalid_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./invalid_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./alignment_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./alignment_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat3.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat3.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./heuristic_block_modifiers.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./heuristic_block_modifiers.hh +[ 0%] Built target ost_base_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./distance_rmsd_test.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_rmsd_test.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/show_sidebar_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/show_sidebar_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./global_align.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./global_align.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./correlate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./correlate.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_option.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./compound_lib.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/immutable_preset_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_preset_info_handler.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_def.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_crd_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh [ 0%] Built target ost_config -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mae_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mae_handler.hh +[ 0%] Built target ost_db_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hhblits3.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits3.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./ptr_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./ptr_observer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./ligand_scoring.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./ligand_scoring.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat4.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat4.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cartoon_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/site_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/site_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./superpose_frames.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./interaction.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./interaction.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./ins_del.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_frequency_domain.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./cross_correlate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./cross_correlate.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/init_inspector.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/init_inspector.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_factory.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_factory.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pqr_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pqr_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./blast.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./blast.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./log.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./log.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./dockq.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./dockq.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./sequence_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./stdint.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./stdint.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset.py -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./rule_based.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./rule_based.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_option.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat4_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./trajectory_analysis.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./invalid_sequence.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./density_slice.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./density_slice.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 0%] Built target scene_icons +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_path.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_path.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/split_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/split_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./filter_clashes.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./settings.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./settings.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_verbose_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mmcif_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./stdint_msc.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./stdint_msc.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./local_align.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./local_align.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./structure_analysis.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./circular_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./circular_iterator.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./views_from_sequences.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/remote.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/remote.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./item_type.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type.hh -[ 0%] Built target ost_bindings_pymod -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./dft.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./dft.hh -[ 0%] Built target ost_mol_alg_pymod -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/fragment_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./density_slice.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./density_slice.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./rule_based.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./rule_based.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_options_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./range.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./range.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_frequency_domain.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/inspector_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/inspector_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mae_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mae_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./cadscore.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./cadscore.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/dihedral.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/dihedral.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./log_sink.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./log_sink.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./aligned_region.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_region.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/stereo_data.json /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/stereo_data.json +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_set.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_set.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec2.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec2.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/warning_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/warning_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./construct_cbeta.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./simulation.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./simulation.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./constants.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./constants.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./consistency_checks.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/debug_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./profile_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./profile_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./minimal_compound_lib.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./merge_pairwise_alignments.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./geom_info_conversion.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_spatial_domain.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/fragment_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./pdbize.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fft.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fft.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_editor_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_list_model.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./dft.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./dft.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/manipulator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/manipulator.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./minimal_compound_lib.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/map_level_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/map_level_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mmcif_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./kclust.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./kclust.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./profile.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./profile.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./aligned_column.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./compound_lib_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_visitor.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/debug_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec3.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec3.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/refresh.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/refresh.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./clash_score.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./modeller.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./modeller.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./item_type_cast.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type_cast.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_ast.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./adjacency_bitmap.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite2.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fftw_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fftw_helper.hh -[ 0%] Built target ost_seq_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_editor_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fft.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fft.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_options_win.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./observer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./consistency_checks.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_ast_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./compound_lib_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_handler.hh +[ 0%] Built target ost_mol_alg_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./dyn_cast.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./dyn_cast.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./ialign.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./ialign.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./aligned_column_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_verbose_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec4.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec4.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./ring_finder.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./ring_finder.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./units.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./units.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite3.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/trace_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fill.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fill.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./trajectory_analysis.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./observer.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./pair_subst_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pdb_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pdb_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_algorithm.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_info_handler.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./state_extractor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./state_extractor.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./contact_overlap.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fftw_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fftw_helper.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/mouse_event.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh -[ 0%] Built target ost_info_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./message.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./message.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_writer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/remote.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/remote.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_spatial_domain.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./ring_finder.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./ring_finder.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./stdint.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./stdint.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./mmseqs2.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./mmseqs2.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/fragment_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./invalid_sequence.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./item_type.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type.hh +[ 0%] Built target scene_icons +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./structure_analysis.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./state_extractor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./state_extractor.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./semiglobal_align.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./filter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./filter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fill.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fill.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/map_tool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/map_tool.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_editor_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_list_model.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/line_trace_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_visitor_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./dockq.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dockq.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pdb_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pdb_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./stdint_msc.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./stdint_msc.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/fragment_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./views_from_sequences.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./geom_info_conversion.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat2_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/trace_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./consistency_checks.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./system_creator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./system_creator.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/map_tool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/map_tool.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./domain_find.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite2_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_list_model.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_sdf_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./sequence_identity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_identity.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./platform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./platform.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/backbone_trace.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./filter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./filter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_algorithm.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_editor_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/align_properties_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh [ 0%] Built target ost_conop_headers +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./range.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./range.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_writer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_ast.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./profile_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./profile_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/line_trace_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat3_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./item_type_cast.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type_cast.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./pdbize.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./topology_creator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology_creator.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/align_properties_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fourier_filters.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./similarity_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite3_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./sequence_similarity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./string_ref.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./string_ref.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/residue_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_reader.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/index.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/index.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_detail.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./index.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./index.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fourier_filters.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_visitor_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_info_handler.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_row.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_row.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./aligned_cuboid.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh +[ 0%] Built target ost_bindings_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_sdf_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_ast_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./module_config.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/backbone_trace.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat4_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./adjacency_bitmap.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./index.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./index.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./subst_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_list_model.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/background_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/index.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/index.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./gaussian_gradient_magnitude.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/render_mode_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_mode_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./accessibility.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./accessibility.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./pod_vector.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./pod_vector.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/residue_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl_fw.hh +[ 0%] Built target ost_seq_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./units.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./units.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl.hh +[ 0%] Built target ost_info_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_detail.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./circular_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./circular_iterator.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./consistency_checks.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./variance_map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./topology.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/conservation_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/type_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/type_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./gaussian.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./message.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./message.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_writer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/background_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec_mat_predicates.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./constants.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./constants.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./topology.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./variance_map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/render_op.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_op.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./sec_struct.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_struct.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./fixed_string.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./fixed_string.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/surface_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./gaussian.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/value_holder.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/value_holder.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/conservation_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/save_entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/save_entity.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./quat.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./quat.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/trace_renderer_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./contact_overlap.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/render_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_options_widget.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./steep.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./steep.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./tri_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./tri_matrix.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/surface_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./gaussian_laplacian.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/painter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/load_entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_entity.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./algorithm.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./algorithm.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./transform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./transform.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/connect_renderer_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/render_mode_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_mode_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/value_holder.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/value_holder.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./gaussian_laplacian.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/save_entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/save_entity.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./platform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./platform.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/residue_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/trace_renderer_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./domain_find.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./nonstandard.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./nonstandard.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/scene_observer_impl.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_observer_impl.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/surface_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./boost_filesystem_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/secstr_row.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/secstr_row.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/render_op.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_op.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./algorithm.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./algorithm.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./highest_peak_search_3d.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./circle_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./circle_mask.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./point_cloud.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./point_cloud.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/mapped_property.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./hmm_pseudo_counts.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/load_entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_entity.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./string_ref.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./string_ref.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/residue_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite2.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/connect_renderer_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./similarity_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh [ 0%] Built target ost_mol_mm_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./molck.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./molck.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./histogram.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./histogram.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/load_surface.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_surface.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./paged_array.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./paged_array.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./hmm_pseudo_counts.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_secstr_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_secstr_painter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./composite_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./composite_mask.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/scene_selection_helper.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_selection_helper.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./hmm_score.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_renderer_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./circle_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./circle_mask.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./histogram.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./histogram.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/render_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_options_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/surface_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./pod_vector.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./pod_vector.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/surface_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite3.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/mapped_property.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./accessibility.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./accessibility.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_selection_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_selection_painter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/surface_io_msms_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./hmm_score.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./composite_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./composite_mask.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./line_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/scene_observer_impl.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_observer_impl.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/load_surface.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_surface.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./fixed_string.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./fixed_string.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/surface_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_renderer_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./sec_struct.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_struct.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_text_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_text_painter.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./data_algorithm.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./data_algorithm.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/simple_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/simple_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./find_membrane.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./atom_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_base.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 0%] Built target ost_base_headers -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/tabulated_trig.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_text_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_text_painter.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./local_sigma_threshold.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/sline_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/sline_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./entity_to_density.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./data_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./data_observer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/scene_selection_helper.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_selection_helper.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/surface_io_msms_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./tri_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./tri_matrix.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite2_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/tabulated_trig.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./nonstandard.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./nonstandard.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_delegate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh [ 0%] Built target ost_seq_alg_headers -[ 0%] Built target ost_geom_headers -make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/fast_spheres.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_str.hh -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./atom_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/geom/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./data_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./data_observer.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./mask_image.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./mask_image.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_delegate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/toolbar_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/toolbar_options_widget.py -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./data_types.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./data_types.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./atom_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_view.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_str.hh -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/simple_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/simple_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./boost_filesystem_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite3_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/fast_spheres.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./molck.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./molck.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_model.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_model.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./data_types.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./data_types.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./negate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./negate.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/trace_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/trace_widget.py -[ 0%] Built target ost_mol_alg_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/sline_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/sline_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_str.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./paged_array.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./paged_array.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./aligned_cuboid.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./atom_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./find_membrane.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./data.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./data.hh -[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat2.cc.o -[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat4.cc.o -[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vec3.cc.o -[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat3.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/stereochemical_params_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/line_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_row.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_row.hh -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/mat2.cc -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/mat3.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./bond_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/mat4.cc -[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat2_op.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./normalizer_factory.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/toolbar_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/toolbar_options_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_str.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec_mat_predicates.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./atom_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/line_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./entity_to_density.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./norm.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_search_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./debug.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./debug.hh -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/vec3.cc -[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat3_op.cc.o -[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/tube_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/tube_widget.py -[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3.cc.o -[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/vecmat2_op.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/omf.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh -[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2_op.cc.o -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/trace_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/trace_widget.py +[ 0%] Built target ost_base_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/stereochemical_params_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different 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-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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/vecmat3_op.cc -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/vecmat4_op.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./bond_table.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_table.hh -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/quat.cc.o +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./dllexport.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./dllexport.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_search_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different 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/build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2.cc -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/composite3.cc -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/composite2_op.cc -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/composite3_op.cc -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/load_map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/load_map.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/uniform_color_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/uniform_color_widget.py -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/quat.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./extent_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_iterator.hh -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/transform.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chain_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_base.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_table_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_table_view.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./normalizer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_df3_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/tube_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/tube_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/omf.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./bond_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./transform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./transform.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/cpk_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/visibility_op.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/visibility_op.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chain_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/simple_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh +[ 0%] Built target ost_mol_alg_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./extent_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_iterator.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_viewer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/image_format.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/image_format.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./norm_linear.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/uniform_color_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/uniform_color_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/load_map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/load_map.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./bond_table.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_table.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./point_cloud.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./point_cloud.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/simple_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./extent_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_mask.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/line_trace_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/line_trace_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/sline_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/tick_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/tick_painter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dx_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chain_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_view.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./norm_log.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_log.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./extent.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./extent.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/wireframe_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/wireframe_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_spi_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chain_type.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_type.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/line_trace_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/query_editor.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/query_editor.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/visibility_op.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/visibility_op.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_df3_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chain_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/sline_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/title_row.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/title_row.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./extent.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./extent.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./norm_od.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_od.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_situs_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/line_trace_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/line_trace_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/image_format.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/image_format.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chain_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/line_trace_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_factory.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_factory.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chem_class.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_class.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/alignment_view_object.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/alignment_view_object.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/wireframe_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/wireframe_widget.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./power_spectrum.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dx_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh +[ 0%] Built target ost_geom_headers +make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/depend +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chain_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_view.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/cartoon_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/alignment_view_object.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/alignment_view_object.hh +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/geom/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chem_type.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_type.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/trace_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_mrc_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh -[ 1%] Built target ost_gui_scene_pymod -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_handle_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_view_object.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_view_object.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./coord_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_group.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/query_editor.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/query_editor.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./randomize.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./randomize.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle.hh -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/aligned_cuboid.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_spi_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chain_type.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_type.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/trace_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_handle_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_view_object.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_view_object.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./smooth_mask_image.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_situs_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chem_class.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_class.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh -cd 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-I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/mat4.cc +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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 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-I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/mat3.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 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-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-2.5.0/modules/geom/src/composite3_op.cc +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vec3.cc.o +[ 1%] Built target ost_gui_scene_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./stat.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/main_thread_runner.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/main_thread_runner.hh +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat3_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/vec3.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/vecmat3_op.cc +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/quat.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/composite2.cc +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/quat.cc +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/aligned_cuboid.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/point_cloud.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/transform.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chem_type.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_type.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/output_redirector.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./stat_accumulator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./coord_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_group.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_mrc_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/completer_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/completer_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./stat_min_max.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./coord_source.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_source.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_list.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_list.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dat_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./smooth_mask_image.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/uniform_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./in_mem_coord_source.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./in_mem_coord_source.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_list.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_list.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/main_thread_runner.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/main_thread_runner.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./coord_frame.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_frame.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/output_redirector.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./editor_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/dir_model.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./threshold.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./threshold.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_ipl_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_state_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/uniform_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./stat.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./editor_type_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/completer_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/completer_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./coord_frame.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_frame.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_jpk_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/gutter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_state.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./stat_accumulator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./stat_min_max.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/dir_model.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transcendentals.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./editor_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/entity_view_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_nanoscope_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./editor_type_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/path_completer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./mol.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./mol.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./threshold.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./threshold.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/gutter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_context_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transform_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/basic_gradient_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/basic_gradient_color_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transcendentals.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_png_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./inverted_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./inverted_mask.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/path_completer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_level_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/map_handle_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_context_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dm3_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_completer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./map.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transform_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./render_pass.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_pass.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_completer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_tiff_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_base_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_level_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./alg_transform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_transform.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dm3_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_base_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_shell.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./bitmap_io.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/map_handle_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./alg_mirror.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_mirror.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/tiff_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/tiff_util.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_tiff_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_handle.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./render_pass.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_pass.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_shell_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_observer_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_shell_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./alg_shift.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_property_mapper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./collada_exporter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/tiff_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/tiff_util.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./bitmap_io.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_shell_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./discrete_shrink.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/jpk_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/jpk_util.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_observer_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./collada_exporter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_visitor.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_tokenizer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_tokenizer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/sequence_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./color.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./color.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transformation_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_property_mapper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_view.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./discrete_shrink.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/sequence_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_syntax_highlighter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/text_logger.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transformation_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_visitor_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./entity_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_syntax_highlighter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/fasta_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./normalizer_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gl_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_helper.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_interpreter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transformations.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformations.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./handle_type_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pir_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_interpreter_worker.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fractional_shift.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fractional_shift.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./entity_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./normalizer_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/text_logger.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/promod_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_visitor_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gl_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_helper.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./module_config.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./normalizer_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_interpreter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/profile_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./handle_type_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx.hh -In file included from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2.cc:23: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/modules/geom/src/def.hh:26, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./ics_editor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./ics_editor.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/promod_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./null_data.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./null_data.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_shell_text_document_layout.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./polar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./polar.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_interpreter_worker.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./not_connected_error.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./not_connected_error.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/profile_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./ics_editor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./ics_editor.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./observable.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./observable.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/shell_history.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./property_id.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./property_id.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./polar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./polar.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/hhm_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/hhm_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./paste_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./paste_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/state_machine.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./query.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./query.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./line_average.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_average.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_node_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./peak.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./peak.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_shell_text_document_layout.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./paste_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./paste_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pssm_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pssm_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/state.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./query_error.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_error.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_node_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./not_connected_error.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./not_connected_error.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./rscrosscorr.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./rscrosscorr.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/shell_history.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_node_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./peak.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./peak.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/clustal_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/transition.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./phase.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./phase.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./query_state.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_state.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./property_id.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./property_id.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/state_machine.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_node_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./query.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./query.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./phase.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./phase.hh +[ 1%] Built target ost_img_alg_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/state.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/load.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/load.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./physical_units.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./physical_units.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./query_error.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_error.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_object_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/transition_guard.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/transition.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/save.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/save.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./pixel_sampling.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./pixel_sampling.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/transition_guard.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./query_state.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_state.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./binary_data_sink.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_sink.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_object.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./point_list.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./point_list.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/button_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_bar.hh -[ 1%] Built target ost_img_alg_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./physical_units.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./physical_units.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./io_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./io_manager.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./residue_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./point.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./point.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_object_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/drop_box.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/drop_box.hh -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./binary_data_sink.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_sink.hh -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/geom/src/point_cloud.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./binary_data_source.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_source.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./polygon_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./polygon_mask.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_prim.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/panel_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./pixel_sampling.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./pixel_sampling.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/panel_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_manager.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./residue_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/panel_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./progress.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./progress.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./symmetry_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./io_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./io_manager.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./point_list.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./point_list.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/panel_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_manager.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./residue_prop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_prop.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./size.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./size.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/bottom_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/bottom_bar.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_test_object.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./binary_data_source.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_source.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./residue_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_view.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./point.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./point.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./container_serialization.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./container_serialization.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./spherical_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./spherical_mask.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/button_box.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_box.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./glwin_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glwin_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./swap_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./swap_util.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./util.cc /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./util.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./sec_structure.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./sec_structure.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./polygon_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./polygon_mask.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/event_button.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/event_button.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./input.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./input.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/event_button.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/event_button.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./io_utils.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./io_utils.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./util.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./spatial_organizer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./container_serialization.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./container_serialization.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./progress.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./progress.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/panel_widget_container.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_widget_container.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./surface.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./prim_list.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./prim_list.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./size.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./size.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./swap_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./swap_util.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./io_exception.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./io_exception.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./value_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./value_util.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/panel_bar_widget_holder.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar_widget_holder.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./surface_builder.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_builder.hh -In file included from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2_op.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2_op.cc:24: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./io_utils.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./io_utils.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./spherical_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./spherical_mask.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./surface.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./vecmat.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./vecmat.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./convert.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./convert.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./scene.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/side_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/side_bar.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./io_exception.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./io_exception.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./surface_builder.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_builder.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_info_convert.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_info_convert.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./converting_streams.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./converting_streams.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./selection.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./selection.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./builder.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./builder.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/splitter_panel_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/splitter_panel_bar.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./util.cc /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./util.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./selection.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./selection.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./formatted_line.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./formatted_line.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./surface.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./surface.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/tabbed_panel_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/tabbed_panel_bar.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./convert.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./convert.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./surface_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./util.hh +[ 1%] Built target ost_img_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./texture.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./texture.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/chemdict_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./chemdict_parser.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/context_menu.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/context_menu.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./surface.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./surface.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./converting_streams.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./converting_streams.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./value_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./value_util.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./surface_prop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_prop.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./vertex_array.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/star_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./star_parser.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/current_selection_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/current_selection_node.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./texture.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./texture.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./torsion_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./torsion_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./formatted_line.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./formatted_line.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./vecmat.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./vecmat.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/mmcif_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./vertex_array_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/custom_part_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/custom_part_node.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./transfer_connectivity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./transfer_connectivity.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./vertex_array.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_info_convert.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_info_convert.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/chemdict_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./chemdict_parser.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./scene_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene_observer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/mmcif_info.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_info.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/entity_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_node.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./vertex_array_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./query_view_wrapper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_view_wrapper.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/star_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./star_parser.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./scene_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene_observer.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/mmcif_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_reader.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gl_include.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_include.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/io_profile.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./io_profile.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/entity_part_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_part_node.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gl_include.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_include.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./view_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./glext_include.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glext_include.hh -[ 1%] Built target ost_img_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/mmcif_info.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_info.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./render_mode.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_mode.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/gfx_scene_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/gfx_scene_node.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/dcd_io.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./dcd_io.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./view_type_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_type_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./material.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./material.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/io_profile.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./io_profile.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./view_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gradient.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./render_mode.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_mode.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_crd_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/label_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/label_node.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gradient_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/dcd_io.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./dcd_io.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./xcs_editor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./xcs_editor.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./view_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./material.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./material.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_pqr_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/root_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/root_node.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./primitives.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./primitives.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./bounding_box.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./bounding_box.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_crd_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./povray_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./xcs_editor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./xcs_editor.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gradient.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_mae_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/render_mode_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_mode_node.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./bounding_box.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./bounding_box.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_mmcif_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gradient_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/render_modes_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_modes_node.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./transform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./transform.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./povray.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/scene_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_pqr_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/render_modes_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_modes_node.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./primitives.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./primitives.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/pdb_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/scene_win.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_mae_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./exporter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter.hh [ 1%] Built target ost_mol_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/scene_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_mmcif_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./exporter_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gost_exporter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/scene_win.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/pdb_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_reader.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./color_ops/map_handle_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/scene_win_model.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_pdb_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./povray_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/scene_win_model.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/pdb_writer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_writer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./povray.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/messages/message_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_widget.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./map_iso.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./map_slab.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_slab.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_sdf_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/messages/message_box_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_box_widget.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./map_iso_prop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_sdf_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./exporter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/sdf_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_reader.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/messages/log_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/log_reader.hh -[ 1%] Built target ost_gfx_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./exporter_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/sdf_writer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_writer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gost_exporter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/argand.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/argand.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/save_entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./save_entity.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./color_ops/map_handle_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/data_viewer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./map_iso.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/data_viewer_panel.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/load_entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./load_entity.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/surface_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/data_viewer_panel.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/load_surface.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./load_surface.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/data_viewer_panel_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/surface_io_msms_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./map_slab.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_slab.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./map_iso_prop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/load_surface.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./load_surface.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/draw_overlay.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/draw_overlay.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/pdb_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_str.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/drawing_functions.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/drawing_functions.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/sdf_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_str.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/mmcif_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_str.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/surface_io_msms_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh +[ 1%] Built target ost_gfx_headers cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/fft_panel.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/fft_panel.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/stereochemical_params_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/pdb_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_str.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/info_panel.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/info_panel.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/omf.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./omf.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/sdf_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_str.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/img2qt.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/img2qt.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/sequence_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/mmcif_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_str.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/stereochemical_params_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/mask_overlay.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/mask_overlay.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/fasta_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/omf.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./omf.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/null_overlay.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/null_overlay.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/sequence_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/fasta_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/pir_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pir_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/promod_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./promod_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_base_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/promod_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./promod_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/profile_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./profile_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_manager_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/hhm_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_manager_gui.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_gui.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/pssm_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_manager_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_observer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/pssm_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/clustal_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./clustal_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/pointlist_overlay.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh +In file included from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2.cc:23: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/modules/geom/src/def.hh:26, + from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/load.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./load.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/pointlist_overlay_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/save.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./save.hh +In file included from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2_op.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2_op.cc:24: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/strategies.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/save.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./save.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/load_map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./load_map.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/strategies_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_df3_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_df3_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/viewer_normalizer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/viewer_normalizer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/image_format.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./image_format.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./file_browser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_browser.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/image_format.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./image_format.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./file_type_dialog.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_type_dialog.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_dx_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dx_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./file_viewer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_viewer.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_spi_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_spi_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./gl_canvas.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_canvas.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./file_viewer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_viewer.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_situs_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_situs_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./gl_canvas.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_canvas.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./gl_win.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_win.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_mrc_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_mrc_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./scene_menu.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_menu.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./gosty_app.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./gosty_app.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_mrc_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_mrc_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_dat_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dat_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./admin.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./admin.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./gosty_app.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./gosty_app.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_ipl_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_ipl_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./admin.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./admin.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./module_config.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_jpk_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_jpk_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./main.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./main.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_nanoscope_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_nanoscope_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_png_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./main_area.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_area.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_png_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_dm3_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dm3_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./perspective.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./perspective.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_tiff_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_tiff_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./scene_selection.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_selection.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./main_window.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_window.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/tiff_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./tiff_util.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/jpk_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./jpk_util.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./dock_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/jpk_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./jpk_util.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./dock_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh [ 1%] Built target ost_io_headers @@ -3812,84 +3848,107 @@ cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod/CMakeFiles/_ost_geom.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 1%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log.cc.o +[ 1%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/generic_property.cc.o +[ 1%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec3.cc.o [ 1%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o -[ 1%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat4.cc.o -[ 1%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/wrap_geom.cc.o +[ 1%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log_sink.cc.o [ 1%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o -[ 1%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o [ 1%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec4.cc.o -[ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec3.cc.o -[ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec2.cc.o -[ 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_composite2.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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 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-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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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_vec3.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec3.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec3.cc -[ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat2.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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_vecmat3_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat3_op.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/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_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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/src/CMakeFiles/ost_base.dir/generic_property.cc.o -MF CMakeFiles/ost_base.dir/generic_property.cc.o.d -o CMakeFiles/ost_base.dir/generic_property.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/generic_property.cc -[ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -[ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log.cc.o -[ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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_vec3.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec3.cc.o -c 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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-2.5.0/modules/geom/pymod/export_composite2_op.cc [ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/units.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/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_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -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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modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o -MF CMakeFiles/_ost_geom.dir/export_quat.cc.o.d -o CMakeFiles/_ost_geom.dir/export_quat.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_quat.cc [ 5%] Linking CXX shared library ../../../stage/lib/libost_base.so cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0=. -fstack-protector-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.2.5 -o ../../../stage/lib/libost_base.so.2.5.0 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 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-ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/info/src/geom_info_conversion.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/info/src/info_verbose_visitor.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec3.cc:22: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/geom_info_conversion.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec3.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_handle.hh:31, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -3899,40 +3958,21 @@ /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-2.5.0/obj-x86_64-linux-gnu' -[ 5%] Built target ost_base -make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/info/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src 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-I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/info/src/info_impl.cc -[ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_group.cc.o -[ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/info/src/info_handle.cc -[ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_item.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/info/src/info_group.cc -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/info/src/info_item.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat4_op.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat4_op.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_handle.hh:31, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -3945,7 +3985,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3_op.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -3959,7 +3999,7 @@ 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-2.5.0/modules/geom/pymod/export_composite2.cc:19: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -3972,7 +4012,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/wrap_geom.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_quat.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -3986,7 +4026,7 @@ 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-2.5.0/modules/geom/pymod/wrap_geom.cc:19: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -3999,7 +4039,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3_op.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec4.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4013,17 +4053,20 @@ 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-2.5.0/modules/geom/pymod/export_composite3_op.cc:21: + from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat3_op.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat3.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4037,10 +4080,7 @@ 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-2.5.0/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 - | ^~~~~~~~ + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4053,21 +4093,20 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec4.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_set.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_set.cc:29: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec4.cc:19: +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-2.5.0/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 | ^~~~~~~~ @@ -4080,7 +4119,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat2_op.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2_op.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4094,7 +4133,7 @@ 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-2.5.0/modules/geom/pymod/export_vecmat2_op.cc:19: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4107,7 +4146,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat3.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4121,7 +4160,7 @@ 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-2.5.0/modules/geom/pymod/export_mat3.cc:19: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4134,7 +4173,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_quat.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec2.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4148,7 +4187,7 @@ 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-2.5.0/modules/geom/pymod/export_quat.cc:19: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4161,21 +4200,19 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec2.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_verbose_visitor.cc:28: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec2.cc:19: +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-2.5.0/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 | ^~~~~~~~ @@ -4188,21 +4225,20 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2_op.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_handle.cc:30: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2_op.cc:21: +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-2.5.0/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 | ^~~~~~~~ @@ -4215,7 +4251,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat2.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/wrap_geom.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4229,7 +4265,7 @@ 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-2.5.0/modules/geom/pymod/export_mat2.cc:19: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4242,7 +4278,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3.cc:21: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat3_op.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4256,7 +4292,7 @@ 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-2.5.0/modules/geom/pymod/export_composite3.cc:19: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4266,23 +4302,24 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_path.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/info/src/info_path.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.cc:27: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat2.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_handle.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info.hh:31: + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4295,7 +4332,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat4.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat4_op.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4309,7 +4346,7 @@ 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-2.5.0/modules/geom/pymod/export_mat4.cc:20: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4319,14 +4356,12 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_set.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/info/src/info_set.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_handle.cc:30: + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_item.cc:31: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4337,7 +4372,7 @@ 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-2.5.0/modules/info/src/info_handle.cc:27: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4347,10 +4382,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_visitor.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/info/src/info_visitor.cc -[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/info/src/geom_info_conversion.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4379,20 +4410,21 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_item.cc:31: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat2_op.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/info/src/info_item.cc:27: +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/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4402,23 +4434,24 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/info/src/info_verbose_visitor.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/geom_info_conversion.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_handle.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:31: + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4431,20 +4464,21 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_set.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_set.cc:29: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec3.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/info/src/info_set.cc:25: +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/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4457,19 +4491,21 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_verbose_visitor.cc:28: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat4.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/info/src/info_verbose_visitor.cc:25: +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/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4492,13 +4528,13 @@ 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-2.5.0/obj-x86_64-linux-gnu' [ 6%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o -[ 6%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o -[ 6%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o [ 6%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/base/pymod/export_units.cc -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/base/pymod/wrap_base.cc +[ 6%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o +[ 6%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/base/pymod/export_logger.cc cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/base/pymod/export_range.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/base/pymod/wrap_base.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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-2.5.0/modules/base/pymod/export_units.cc [ 6%] Linking CXX shared library ../../../stage/lib/libost_info.so cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0=. -fstack-protector-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.2.5 -o ../../../stage/lib/libost_info.so.2.5.0 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-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/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.2.5.0 /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.2.5.0 /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 @@ -4508,56 +4544,109 @@ 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-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/build +make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_algorithm.cc.o -[ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/circle_mask.cc.o [ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/composite_mask.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/data_algorithm.cc -[ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o -[ 6%] 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/extent_iterator.cc.o -[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o -[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o -[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o -[ 7%] Building CXX object 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-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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/atom_base.cc +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_iterator.cc.o +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent.cc.o +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/circle_mask.cc cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/composite_mask.cc +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/data_algorithm.cc +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/data_observer.cc -[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/data.cc -[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/atom_handle.cc cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/extent_iterator.cc +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/extent_mask.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/atom_view.cc +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/bond_handle.cc +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/chain_base.cc +[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask.cc.o +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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_handle.cc.o -MF CMakeFiles/ost_mol.dir/chain_handle.cc.o.d -o CMakeFiles/ost_mol.dir/chain_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/chain_view.cc cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/extent.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/chain_type.cc cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/image_factory.cc -[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o +[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/coord_frame.cc cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/image_handle.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/coord_group.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/editor_base.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/entity_base.cc +[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/image_impl.cc +[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/entity_handle.cc cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/image_list.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/entity_observer.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/entity_property_mapper.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK 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CMakeFiles/ost_img.dir/inverted_mask.cc.o.d -o CMakeFiles/ost_img.dir/inverted_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/inverted_mask.cc cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/map.cc -[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/mask_base.cc -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/atom_base.cc -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o +[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ 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/usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/mask_op.cc +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o +[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT 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/usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/mask.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/observable.cc +cd 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-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-2.5.0/modules/img/base/src/paste_impl.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/peak.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/phase.cc +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/physical_units.cc +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/pixel_sampling.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/pixel_sampling.cc +[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/ics_editor.cc +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/point_list.cc +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/point.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent.cc:31: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_list.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_list.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4566,9 +4655,9 @@ 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-2.5.0/modules/img/base/src/extent.cc:28: + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4603,58 +4692,10 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/inverted_mask.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/inverted_mask.cc:24: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data.cc:29: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_list.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_list.cc:26: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent.cc:31: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4663,9 +4704,9 @@ 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-2.5.0/modules/img/base/src/image_list.cc:24: + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4705,16 +4746,23 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/composite_mask.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/composite_mask.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_factory.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state_fw.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_impl.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: +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-2.5.0/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 | ^~~~~~~~ @@ -4727,24 +4775,19 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_factory.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state_fw.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_impl.cc:21: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent_mask.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent_mask.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/base/src/image_impl.hh:30: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4758,15 +4801,17 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4808,19 +4853,14 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent_mask.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent_mask.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent.hh:30: +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-2.5.0/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 | ^~~~~~~~ @@ -4834,8 +4874,8 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/circle_mask.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/circle_mask.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4852,30 +4892,20 @@ /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/mask.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/mask.cc -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/observable.cc -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/paste_impl.cc -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/peak.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_factory.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_factory.cc:29: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/inverted_mask.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/inverted_mask.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_factory.cc:27: +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-2.5.0/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 | ^~~~~~~~ @@ -4885,26 +4915,20 @@ /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/phase.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/phase.cc -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/physical_units.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_handle.hh:38, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_handle.cc:31: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/observable.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/observable.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_handle.cc:27: +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-2.5.0/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 | ^~~~~~~~ @@ -4917,22 +4941,17 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/composite_mask.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_op.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/base/src/mask_base_fw.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_op.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_op.cc:21: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4945,17 +4964,18 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_base.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data.cc:29: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_base.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -4965,40 +4985,22 @@ /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/pixel_sampling.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/pixel_sampling.cc -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/point_list.cc -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/point.cc -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/polygon_mask.cc -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/progress.cc -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/spherical_mask.cc -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/mask_info_convert.cc -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/image_state/image_state_factory.cc -[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/atom_handle.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/observable.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/observable.cc:27: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_factory.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_factory.cc:29: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/observable.hh:30: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5012,20 +5014,16 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_algorithm.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/paste_impl.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/paste_impl.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/composite_mask.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/composite_mask.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:32: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5038,10 +5036,10 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/in_mem_coord_source.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_group.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -5049,7 +5047,8 @@ from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask.hh:28: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5059,47 +5058,33 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/peak.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/peak.cc:30: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.cc:24: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.cc:31: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/composite_mask.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_op.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.cc:27: +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-2.5.0/modules/img/base/src/mask_base_fw.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_op.hh:24, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5109,24 +5094,22 @@ /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/index.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/image_state/index.cc -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/image_state/image_state_base.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/size.cc:32: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_handle.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/size.cc:27: + 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5139,9 +5122,8 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/pixel_sampling.cc:27: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_handle.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -5149,8 +5131,9 @@ from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/pixel_sampling.hh:30: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_handle.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5160,21 +5143,19 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/atom_view.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point_list.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point_list.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bond_handle.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/base/src/point.hh:30: + from /usr/include/c++/13/list:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bond_handle.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5184,26 +5165,22 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/raster_image/raster_image.cc -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/bond_handle.cc -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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_handle.cc.o -MF CMakeFiles/ost_mol.dir/chain_handle.cc.o.d -o CMakeFiles/ost_mol.dir/chain_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.cc -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/chain_base.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/in_mem_coord_source.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_frame.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/base/src/polygon_mask.cc:25: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5213,21 +5190,21 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/chain_view.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/spherical_mask.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/spherical_mask.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_property_mapper.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_property_mapper.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5237,20 +5214,13 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/chain_type.cc -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/coord_frame.cc -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/coord_group.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_factory.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_factory.cc:27: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_view.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_view.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -5258,8 +5228,9 @@ from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data_types.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_factory.hh:30: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_view.hh:25, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5269,21 +5240,22 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/editor_base.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_info_convert.cc:28: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_handle.hh:38, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_handle.cc:31: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/base/src/mask_info_convert.cc:25: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5293,23 +5265,28 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/entity_base.cc +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.cc:22: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_handle.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_base.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_handle.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_handle.cc:19: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5319,25 +5296,24 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/entity_handle.cc -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/entity_observer.cc -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/entity_property_mapper.cc -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/entity_view.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/peak.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/peak.cc:30: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/mol/base/src/chain_handle.hh:22: +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-2.5.0/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 | ^~~~~~~~ @@ -5347,26 +5323,23 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/not_connected_error.cc +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/polygon_mask.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_base.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_base.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_view.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/base/src/image_state/image_state_base_fw.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_base.hh:30: +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-2.5.0/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 | ^~~~~~~~ @@ -5376,19 +5349,46 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41: +/build/reproducible-path/openstructure-2.5.0/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 + | ^~~~~~~~ +[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/property_id.cc +[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/query.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/progress.cc +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/size.cc +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/query_error.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/residue_base.cc +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/residue_handle.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/raster_image/raster_image.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/raster_image/raster_image.cc:38: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_algorithm.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/paste_impl.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/paste_impl.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/base/src/raster_image/raster_image.cc:31: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5398,21 +5398,22 @@ /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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/query_state.cc +[ 13%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/spherical_mask.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_base.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/circle_mask.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/circle_mask.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_base.cc:19: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5422,13 +5423,17 @@ /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/residue_view.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/residue_view.cc +[ 13%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/mask_info_convert.cc +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_builder.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/surface_builder.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_view.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_view.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_base.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -5437,8 +5442,8 @@ from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_view.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_view.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5448,22 +5453,30 @@ /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/surface_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/surface_handle.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/in_mem_coord_source.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_group.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/pixel_sampling.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_group.cc:19: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5473,54 +5486,45 @@ /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/entity_visitor.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/entity_visitor.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/in_mem_coord_source.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_frame.cc:27: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point_list.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point_list.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_frame.cc:24: +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-2.5.0/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 | ^~~~~~~~ +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.cc:24: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/transfer_connectivity.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_view.cc:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_base.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/mol/base/src/chain_view.cc:19: + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5530,13 +5534,13 @@ /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/ics_editor.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/ics_editor.cc +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/torsion_handle.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -5545,7 +5549,7 @@ from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.hh:25: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5558,19 +5562,17 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_handle.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.cc:31: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_handle.cc:20: + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5580,19 +5582,29 @@ /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/query_view_wrapper.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/query_view_wrapper.cc +[ 13%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/image_state/image_state_factory.cc +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/view_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/view_op.cc +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/coord_source.cc +[ 13%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/image_state/index.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bond_handle.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_view.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_view.cc:30: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bond_handle.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bond_handle.cc:19: + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5602,71 +5614,54 @@ /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/not_connected_error.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/not_connected_error.cc In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.cc:22: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_view.cc:40: /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_base.cc:20: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41: +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/in_mem_coord_source.cc +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/bounding_box.cc +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.cc:24: /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/property_id.cc -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/query.cc +[ 13%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/image_state/image_state_base.cc +[ 13%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/src/raster_image/raster_image.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/xcs_editor.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/atom_impl.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/chain_impl.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/connector_impl.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/dihedral.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/entity_impl.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_view.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_view.cc:30: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/mol/base/src/entity_view.cc:23: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5676,33 +5671,20 @@ /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-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_view.cc:40: -/build/reproducible-path/openstructure-2.5.0/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 - | ^~~~~~~~ -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/query_error.cc -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/query_state.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_property_mapper.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_property_mapper.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/size.cc:32: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/mol/base/src/entity_property_mapper.hh:28: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5712,24 +5694,19 @@ /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/residue_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/residue_base.cc -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/residue_handle.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/spherical_mask.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/spherical_mask.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.hh:25: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5739,38 +5716,24 @@ /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/residue_view.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/residue_view.cc -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/surface_handle.cc -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_builder.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/surface_builder.cc -In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.cc:24: -/build/reproducible-path/openstructure-2.5.0/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%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/transfer_connectivity.cc -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/torsion_handle.cc -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/query_view_wrapper.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/fragment_impl.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/query_ast.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query.cc:28: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_base.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/mol/base/src/query.cc:23: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5780,26 +5743,22 @@ /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/view_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/view_op.cc -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/coord_source.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/query_impl.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/residue_impl.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_handle.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_builder.cc:23: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_handle.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_builder.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_builder.cc:19: + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5809,6 +5768,10 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/surface_impl.cc +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/torsion_impl.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5833,20 +5796,27 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_handle.cc:26: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/atom_prop.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query_state.cc:22: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_view.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: +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-2.5.0/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 | ^~~~~~~~ @@ -5856,26 +5826,22 @@ /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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_handle.cc:26: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_handle.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_handle.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_builder.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:22: + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_builder.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5885,13 +5851,11 @@ /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/in_mem_coord_source.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/in_mem_coord_source.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_base.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query_state.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -5910,29 +5874,23 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query_state.cc:24: -/build/reproducible-path/openstructure-2.5.0/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%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/bounding_box.cc -[ 13%] Linking CXX shared library ../../../../stage/lib/libost_img.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img.dir/link.txt --verbose=1 In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_view.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/transfer_connectivity.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/transfer_connectivity.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/mol/base/src/residue_view.cc:19: + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5947,18 +5905,13 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/transfer_connectivity.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/transfer_connectivity.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query.cc:28: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/transfer_connectivity.hh:23: + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -5968,13 +5921,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/xcs_editor.cc -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-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.2.5 -o ../../../../stage/lib/libost_img.so.2.5.0 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-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /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 /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 -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/atom_impl.cc -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/chain_impl.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6004,30 +5950,23 @@ /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-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5 ../../../../stage/lib/libost_img.so -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 15%] Built target ost_img -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/connector_impl.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/view_op.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_factory.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_factory.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/mol/base/src/view_op.cc:24: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data_types.hh:30, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6040,8 +5979,10 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/torsion_handle.cc:22: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/in_mem_coord_source.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/in_mem_coord_source.cc:1: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -6052,9 +5993,7 @@ 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/torsion_handle.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/torsion_handle.cc:19: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6067,19 +6006,21 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_source.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/torsion_handle.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_source.cc:23: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/torsion_handle.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6089,35 +6030,14 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/view_op.cc:27: -/build/reproducible-path/openstructure-2.5.0/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 - | ^~~~~~~~ -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/dihedral.cc -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-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg.dir/DependInfo.cmake "--color=" -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/entity_impl.cc -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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 -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/fragment_impl.cc -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 15%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/anisotropic.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/in_mem_coord_source.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/in_mem_coord_source.cc:1: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_base.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_base.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -6128,7 +6048,8 @@ 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:25: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_base_fw.hh:28, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6138,24 +6059,19 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/query_ast.cc -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/query_impl.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_info_convert.cc:28: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.hh:25: + from /usr/include/c++/13/deque:62, + from /usr/include/c++/13/stack:62, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6165,13 +6081,11 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/residue_impl.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_source.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -6182,7 +6096,7 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl.cc:19: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6192,20 +6106,33 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/surface_impl.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query_state.cc:24: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.cc:23: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/view_op.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/mol/base/src/impl/atom_impl.cc:19: +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-2.5.0/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 | ^~~~~~~~ @@ -6215,32 +6142,59 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.cc:26: +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/view_op.cc:27: /build/reproducible-path/openstructure-2.5.0/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-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.cc:27: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/raster_image/raster_image.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/raster_image/raster_image.cc:38: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/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 | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl.cc:23: -/build/reproducible-path/openstructure-2.5.0/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{ - | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.cc:19: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/torsion_impl.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6270,21 +6224,19 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bounding_box.cc:26: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/mol/base/src/bounding_box.cc:25: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6294,6 +6246,14 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/dihedral.cc:21: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6318,20 +6278,14 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/anisotropic.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/anisotropic.cc:27: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.cc:35: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/alg/src/anisotropic.cc:25: + from /usr/include/c++/13/bits/stl_tree.h:63, + from /usr/include/c++/13/map:62, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6341,6 +6295,22 @@ /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-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.cc:26: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl.cc:23: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6364,16 +6334,37 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/dihedral.cc:21: +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.cc:24: /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.cc:23: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.cc:27: /build/reproducible-path/openstructure-2.5.0/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{ | ^~~~~~~~ @@ -6383,14 +6374,21 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.cc:35: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bounding_box.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/mol/base/src/impl/entity_impl.cc:22: + 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-2.5.0/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 | ^~~~~~~~ @@ -6400,6 +6398,14 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.cc:40: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6424,24 +6430,31 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.cc:40: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl.cc:21: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/src/impl/atom_prop.cc -[ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/auto_correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/auto_correlate.cc -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/convolute.cc.o -MF CMakeFiles/ost_img_alg.dir/convolute.cc.o.d -o CMakeFiles/ost_img_alg.dir/convolute.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/convolute.cc -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/correlate.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/correlate.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/correlate.cc -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/cross_correlate.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6469,18 +6482,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/residue_impl.cc:25: -/build/reproducible-path/openstructure-2.5.0/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 - | ^~~~~~~~ -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/density_slice.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/density_slice.cc -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/dft.cc.o -MF CMakeFiles/ost_img_alg.dir/dft.cc.o.d -o CMakeFiles/ost_img_alg.dir/dft.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/dft.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6506,22 +6507,142 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/residue_impl.cc:25: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl.cc:27: +/build/reproducible-path/openstructure-2.5.0/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 + | ^~~~~~~~ +[ 16%] Linking CXX shared library ../../../../stage/lib/libost_img.so +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0=. -fstack-protector-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.2.5 -o ../../../../stage/lib/libost_img.so.2.5.0 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-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /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 /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-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5 ../../../../stage/lib/libost_img.so +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 16%] Built target ost_img +make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu' +[ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/anisotropic.cc +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/correlate.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/auto_correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/auto_correlate.cc +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/density_slice.cc.o +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/convolute.cc.o -MF CMakeFiles/ost_img_alg.dir/convolute.cc.o.d -o CMakeFiles/ost_img_alg.dir/convolute.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/convolute.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/correlate.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/correlate.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/cross_correlate.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/density_slice.cc +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/dft.cc.o -MF CMakeFiles/ost_img_alg.dir/dft.cc.o.d -o CMakeFiles/ost_img_alg.dir/dft.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/dft.cc +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o +[ 17%] 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-Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/fft.cc +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/fourier_filters.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian.cc +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/gaussian_gradient_magnitude.cc +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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_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-2.5.0/modules/img/alg/src/gaussian_laplacian.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/highest_peak_search_3d.cc.o -MF CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o.d -o CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/highest_peak_search_3d.cc +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/histogram.cc +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/line_iterator.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/local_sigma_threshold.cc.o -MF CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o.d -o CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/local_sigma_threshold.cc +cd 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-D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o -MF CMakeFiles/ost_img_alg.dir/mask_image.cc.o.d -o CMakeFiles/ost_img_alg.dir/mask_image.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/mask_image.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/normalizer.cc +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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 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-isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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_linear.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_linear.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_linear.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/norm_log.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/norm_od.cc +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/power_spectrum.cc +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/randomize.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/smooth_mask_image.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -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-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/stat_min_max.cc +cd /build/reproducible-path/openstructure-2.5.0/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 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/build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_transform.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/alg_mirror.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/alg_shift.cc +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/threshold.cc +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/discrete_shrink.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/transformation_base.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/transformations.cc +cd /build/reproducible-path/openstructure-2.5.0/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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CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fractional_shift.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/polar.cc +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/rscrosscorr.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/line_average.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl.cc:21: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformation_base.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformation_base.cc:25: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/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 + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_iterator.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_iterator.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl.cc:19: + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6531,13 +6652,9 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/fft.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl.cc:27: -/build/reproducible-path/openstructure-2.5.0/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{ - | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6545,20 +6662,17 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/convolute.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/convolute.cc:21: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformation_base.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformations.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformations.cc:29: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6572,12 +6686,10 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/auto_correlate.cc:23: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_average.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_average.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -6585,7 +6697,7 @@ from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/auto_correlate.cc:21: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6595,12 +6707,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/fourier_filters.cc -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian.cc -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/gaussian_gradient_magnitude.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6608,8 +6714,8 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/dft.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/dft.cc:21: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/polar.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/polar.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -6617,8 +6723,7 @@ from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6628,21 +6733,15 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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_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-2.5.0/modules/img/alg/src/gaussian_laplacian.cc -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/highest_peak_search_3d.cc.o -MF CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o.d -o CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/highest_peak_search_3d.cc -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/histogram.cc.o In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/correlate.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/correlate.cc:21: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/dft.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/dft.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -6650,7 +6749,8 @@ from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6660,7 +6760,6 @@ /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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/histogram.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6668,40 +6767,27 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/cross_correlate.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/cross_correlate.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian.hh:36, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_iterator.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/line_iterator.cc -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/local_sigma_threshold.cc.o -MF CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o.d -o CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/local_sigma_threshold.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/density_slice.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/density_slice.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat_min_max.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/normalizer_factory.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -6709,7 +6795,14 @@ from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, + from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6723,49 +6816,43 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.cc:36: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_gradient_magnitude.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_gradient_magnitude.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/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 /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-2.5.0/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 | ^~~~~~~~ -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mask_image.cc.o -MF CMakeFiles/ost_img_alg.dir/mask_image.cc.o.d -o CMakeFiles/ost_img_alg.dir/mask_image.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/mask_image.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fourier_filters.cc:27: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_laplacian.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_laplacian.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/alg/src/fourier_filters.cc:25: + from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6775,26 +6862,24 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/normalizer.cc -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/normalizer_factory.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_iterator.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_iterator.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_transform.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_transform.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:30: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6811,15 +6896,16 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian.cc:27: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/histogram.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/alg/src/gaussian.cc:25: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6836,15 +6922,17 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_gradient_magnitude.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_gradient_magnitude.cc:27: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/cross_correlate.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/cross_correlate.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/alg/src/gaussian_gradient_magnitude.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6883,19 +6971,14 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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_linear.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_linear.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_linear.cc -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/norm_log.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/histogram.cc:27: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/discrete_shrink.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/discrete_shrink.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -6903,7 +6986,7 @@ from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/histogram.cc:25: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6920,42 +7003,42 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_laplacian.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_laplacian.cc:27: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian.hh:36, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/anisotropic.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/anisotropic.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat_min_max.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/normalizer_factory.cc:27: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fourier_filters.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: + from /build/reproducible-path/openstructure-2.5.0/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 + | ^~~~~~~~ +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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6973,19 +7056,16 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/local_sigma_threshold.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/local_sigma_threshold.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_shift.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_shift.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/alg/src/local_sigma_threshold.cc:20: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -6995,8 +7075,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/norm_od.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7004,17 +7082,15 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/normalizer.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/normalizer.cc:26: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat_min_max.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat_min_max.cc:32: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7024,8 +7100,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/power_spectrum.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7034,21 +7108,20 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/mask_image.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_linear.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_linear.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/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 /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-2.5.0/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 | ^~~~~~~~ @@ -7061,8 +7134,8 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_linear.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_linear.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_log.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_log.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7083,14 +7156,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/randomize.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/smooth_mask_image.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/stat.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/stat_min_max.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7099,20 +7164,22 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_log.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_log.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/convolute.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/convolute.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7122,28 +7189,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/alg_transform.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/alg_mirror.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/alg_shift.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/threshold.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/discrete_shrink.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/transformation_base.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/transformations.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/fractional_shift.cc -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/polar.cc -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/rscrosscorr.cc -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/alg/src/line_average.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7152,16 +7197,16 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/power_spectrum.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/correlate.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/correlate.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/power_spectrum.cc:21: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7210,15 +7255,16 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/smooth_mask_image.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/power_spectrum.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7232,15 +7278,20 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformation_base.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformation_base.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/threshold.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/threshold.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/alg/src/transformation_base.hh:30: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7258,8 +7309,7 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_mirror.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_mirror.cc:21: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/mask_image.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7285,8 +7335,7 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/randomize.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/randomize.cc:21: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/smooth_mask_image.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7308,18 +7357,20 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat_min_max.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat_min_max.cc:32: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/randomize.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/randomize.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/alg/src/stat_min_max.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7333,17 +7384,23 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformation_base.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformations.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformations.cc:29: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/local_sigma_threshold.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/local_sigma_threshold.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformations.cc:27: + 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-2.5.0/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 | ^~~~~~~~ @@ -7361,8 +7418,8 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_transform.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_transform.cc:21: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_mirror.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_mirror.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7384,18 +7441,21 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/discrete_shrink.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/discrete_shrink.cc:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.cc:36: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/discrete_shrink.cc:21: + 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-2.5.0/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 | ^~~~~~~~ @@ -7409,19 +7469,18 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/rscrosscorr.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat.cc:32: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7438,15 +7497,17 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat.cc:32: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/normalizer.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/normalizer.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/alg/src/stat.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7464,8 +7525,7 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/threshold.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/threshold.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/rscrosscorr.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7487,10 +7547,12 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_average.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_average.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/auto_correlate.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7498,7 +7560,7 @@ from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:30: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7516,15 +7578,16 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fractional_shift.cc:26: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/density_slice.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/density_slice.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/img/alg/src/fractional_shift.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7542,42 +7605,15 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_shift.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_shift.cc:21: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/polar.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/polar.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fractional_shift.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/polar.hh:23: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7590,12 +7626,12 @@ [ 21%] Linking CXX shared library ../../../../stage/lib/libost_img_alg.so cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0=. -fstack-protector-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.2.5 -o ../../../../stage/lib/libost_img_alg.so.2.5.0 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-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/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.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /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 /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-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img_alg.so.2.5 ../../../../stage/lib/libost_img_alg.so -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 21%] Built target ost_img_alg [ 21%] Linking CXX shared library ../../../../stage/lib/libost_mol.so cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0=. -fstack-protector-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.2.5 -o ../../../../stage/lib/libost_mol.so.2.5.0 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-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /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 /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-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img_alg.so.2.5 ../../../../stage/lib/libost_img_alg.so +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 21%] Built target ost_img_alg cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_mol.so.2.5 ../../../../stage/lib/libost_mol.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 21%] Built target ost_mol @@ -7606,40 +7642,70 @@ 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-2.5.0/obj-x86_64-linux-gnu' [ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_handle.cc.o +[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o [ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o [ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o -[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o +[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o [ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_column.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/seq/base/src/aligned_region.cc -[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/impl/sequence_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_impl.cc -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/impl/sequence_list_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_impl.cc +[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/seq/base/src/sequence_handle.cc [ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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 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-I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/seq/base/src/alignment_handle.cc +cd 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-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_op.cc.o -MF CMakeFiles/ost_seq.dir/sequence_op.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_op.cc cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/seq/base/src/views_from_sequences.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/seq/base/src/profile_handle.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_impl.cc:23: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_handle.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_handle.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:31: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/aligned_region.cc:24: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/integrity_error.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7674,23 +7740,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/alignment_handle.cc:27: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/alignment_handle.cc:32: -/build/reproducible-path/openstructure-2.5.0/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 + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27: +/build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7735,7 +7799,7 @@ from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/integrity_error.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/aligned_region.cc:23: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7753,21 +7817,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/alignment_handle.cc:27: +/build/reproducible-path/openstructure-2.5.0/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 /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, @@ -7799,22 +7857,18 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/views_from_sequences.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/views_from_sequences.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_impl.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/integrity_error.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/views_from_sequences.cc:19: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_handle.hh:31, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7824,14 +7878,20 @@ /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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/alignment_handle.cc:32: +/build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7840,13 +7900,7 @@ from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -7858,22 +7912,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_impl.cc:26: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ @@ -7885,16 +7923,14 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_list.cc:27: + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_impl.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_list.cc:24: +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-2.5.0/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 | ^~~~~~~~ @@ -7904,9 +7940,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 21%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/_ost_base.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_base.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-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/python3.11/dist-packages/ost/_ost_base.so CMakeFiles/_ost_base.dir/wrap_base.cc.o CMakeFiles/_ost_base.dir/export_logger.cc.o CMakeFiles/_ost_base.dir/export_range.cc.o CMakeFiles/_ost_base.dir/export_units.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_base.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.83.0 ../../../stage/lib/libost_geom.so.2.5.0 /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 In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_list.cc:31: /build/reproducible-path/openstructure-2.5.0/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] @@ -7915,56 +7948,30 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 21%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/_ost_base.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_base.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-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/python3.11/dist-packages/ost/_ost_base.so CMakeFiles/_ost_base.dir/wrap_base.cc.o CMakeFiles/_ost_base.dir/export_logger.cc.o CMakeFiles/_ost_base.dir/export_range.cc.o CMakeFiles/_ost_base.dir/export_units.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_base.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.83.0 ../../../stage/lib/libost_geom.so.2.5.0 /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 cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/settings.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.pyc\",\"settings.py\",doraise=True)" +[ 22%] Linking CXX shared library ../../../../stage/lib/libost_seq.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq.dir/link.txt --verbose=1 cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/stutil.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.pyc\",\"stutil.py\",doraise=True)" +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-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.so.2.5 -o ../../../../stage/lib/libost_seq.so.2.5.0 CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o CMakeFiles/ost_seq.dir/sequence_handle.cc.o CMakeFiles/ost_seq.dir/aligned_region.cc.o CMakeFiles/ost_seq.dir/aligned_column.cc.o CMakeFiles/ost_seq.dir/sequence_list.cc.o CMakeFiles/ost_seq.dir/alignment_handle.cc.o CMakeFiles/ost_seq.dir/sequence_op.cc.o CMakeFiles/ost_seq.dir/views_from_sequences.cc.o CMakeFiles/ost_seq.dir/profile_handle.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 /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.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /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 cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/table.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.pyc\",\"table.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/table_selector.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.pyc\",\"table_selector.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/xmlrunner.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.pyc\",\"xmlrunner.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/testutils.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.pyc\",\"testutils.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5 ../../../../stage/lib/libost_seq.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 21%] Built target _ost_base +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/info/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu' -[ 21%] Building CXX object modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o +[ 22%] Building CXX object modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/info/pymod/wrap_info.cc -[ 22%] Linking CXX shared library ../../../../stage/lib/libost_seq.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-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.so.2.5 -o ../../../../stage/lib/libost_seq.so.2.5.0 CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o CMakeFiles/ost_seq.dir/sequence_handle.cc.o CMakeFiles/ost_seq.dir/aligned_region.cc.o CMakeFiles/ost_seq.dir/aligned_column.cc.o CMakeFiles/ost_seq.dir/sequence_list.cc.o CMakeFiles/ost_seq.dir/alignment_handle.cc.o CMakeFiles/ost_seq.dir/sequence_op.cc.o CMakeFiles/ost_seq.dir/views_from_sequences.cc.o CMakeFiles/ost_seq.dir/profile_handle.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 /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.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /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 -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/info/pymod/wrap_info.cc:29: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_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-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5 ../../../../stage/lib/libost_seq.so -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 22%] Built target ost_seq make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/depend make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/depend @@ -7976,52 +7983,199 @@ make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/build -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 22%] Building CXX object modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -[ 22%] 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/usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_seq_alg.dir/entropy.cc.o -MF CMakeFiles/ost_seq_alg.dir/entropy.cc.o.d -o CMakeFiles/ost_seq_alg.dir/entropy.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.cc -[ 22%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/linear_indexer.cc.o -[ 22%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/binary_container.cc.o -[ 22%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/extract_data_helper.cc.o -[ 22%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -[ 22%] Building CXX object 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CMakeFiles/ost_db.dir/binary_container.cc.o.d -o CMakeFiles/ost_db.dir/binary_container.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/src/binary_container.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/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_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_seq_alg.dir/global_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/global_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/global_align.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/global_align.cc +[ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/binary_container.cc.o +[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/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_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 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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-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_db.dir/extract_data_helper.cc.o -MF CMakeFiles/ost_db.dir/extract_data_helper.cc.o.d -o CMakeFiles/ost_db.dir/extract_data_helper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/src/extract_data_helper.cc -[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB 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-fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -MF CMakeFiles/ost_db.dir/sqlite_wrap.cc.o.d -o CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/src/sqlite_wrap.cc -[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/local_align.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DBOOST_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_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_db.dir/linear_indexer.cc.o -MF CMakeFiles/ost_db.dir/linear_indexer.cc.o.d -o CMakeFiles/ost_db.dir/linear_indexer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/src/linear_indexer.cc -[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/distance_map.cc.o -[ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o -[ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/c++ -DBOOST_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_BINDINGS -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_bindings_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -MF CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o.d -o CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DBOOST_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_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -MF CMakeFiles/ost_db.dir/sqlite_wrap.cc.o.d -o CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/src/sqlite_wrap.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/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_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -MF CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o.d -o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/contact_prediction_score.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/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_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o -MF CMakeFiles/ost_seq_alg.dir/conservation.cc.o.d -o CMakeFiles/ost_seq_alg.dir/conservation.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/conservation.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB 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-DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -MF CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o.d -o 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/usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o -MF CMakeFiles/ost_seq_alg.dir/conservation.cc.o.d -o CMakeFiles/ost_seq_alg.dir/conservation.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/conservation.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DBOOST_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_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_db.dir/extract_data_helper.cc.o -MF CMakeFiles/ost_db.dir/extract_data_helper.cc.o.d -o CMakeFiles/ost_db.dir/extract_data_helper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/src/extract_data_helper.cc cd 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-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/src/CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/pair_subst_weight_matrix.cc -[ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/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_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o -MF CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o.d -o CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/sequence_similarity.cc -[ 25%] Building 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-isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o -MF CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o.d -o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/sequence_identity.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/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_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB 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-I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_seq_alg.dir/distance_map.cc.o -MF CMakeFiles/ost_seq_alg.dir/distance_map.cc.o.d -o CMakeFiles/ost_seq_alg.dir/distance_map.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/distance_map.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK 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-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/src/CMakeFiles/ost_seq_alg.dir/variance_map.cc.o -MF CMakeFiles/ost_seq_alg.dir/variance_map.cc.o.d -o CMakeFiles/ost_seq_alg.dir/variance_map.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/variance_map.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/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_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o -MF CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o.d -o CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/hmm_pseudo_counts.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/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_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -MF CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o.d -o CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/hmm_score.cc +In file included from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:7, + from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:20: +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NW.h: In function 'void NWDP_SE(bool**, double**, double**, double**, int, int, double, double, int*, int)': +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NW.h:275:9: warning: unused variable 'int_min' [-Wunused-variable] + 275 | int int_min=L*(gap_open-1); + | ^~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NW.h:287:9: warning: unused variable 'k' [-Wunused-variable] + 287 | int k=0; + | ^ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:9: +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h: In function 'int NWalign_main(const char*, const char*, int, int, std::string&, std::string&, int, int*, int, int)': +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:415:41: warning: array subscript has type 'char' [-Wchar-subscripts] + 415 | else S[i][j]=BLOSUM[seqx[i-1]][seqy[j-1]]; + | ~~~~~~~~^ +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:415:52: warning: array subscript has type 'char' [-Wchar-subscripts] + 415 | else S[i][j]=BLOSUM[seqx[i-1]][seqy[j-1]]; + | ~~~~~~~~^ +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h: In function 'void get_seqID(const std::string&, const std::string&, std::string&, double&, int&)': +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:458:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 458 | for (int i=0;i >&, char*, char*, std::vector >, std::vector >, std::vector, std::vector, int, int)': +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:697:14: warning: statement has no effect [-Wunused-value] + 697 | for (i;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 878 | for (i=0;i >&, const std::vector >&, std::string, std::string)': +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:1604:38: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'std::map, int>::mapped_type' {aka 'int'} [-Wsign-compare] + 1604 | if (atom_site_pos==_atom_site["Cartn_x"]) +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:1607:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'std::map, int>::mapped_type' {aka 'int'} [-Wsign-compare] + 1607 | else if (atom_site_pos==_atom_site["Cartn_y"]) +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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_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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/semiglobal_align.cc:19: + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -8052,15 +8202,46 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:7, - from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:20: -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NW.h: In function 'void NWDP_SE(bool**, double**, double**, double**, int, int, double, double, int*, int)': -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NW.h:275:9: warning: unused variable 'int_min' [-Wunused-variable] - 275 | int int_min=L*(gap_open-1); - | ^~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NW.h:287:9: warning: unused variable 'k' [-Wunused-variable] - 287 | int k=0; - | ^ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.cc:21: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/modules/seq/alg/src/entropy.cc:24: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, + from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:27: /build/reproducible-path/openstructure-2.5.0/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-2.5.0/modules/bindings/src/USalign/TMalign.h:9: -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h: In function 'int NWalign_main(const char*, const char*, int, int, std::string&, std::string&, int, int*, int, int)': -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:415:41: warning: array subscript has type 'char' [-Wchar-subscripts] - 415 | else S[i][j]=BLOSUM[seqx[i-1]][seqy[j-1]]; - | ~~~~~~~~^ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:415:52: warning: array subscript has type 'char' [-Wchar-subscripts] - 415 | else S[i][j]=BLOSUM[seqx[i-1]][seqy[j-1]]; - | ~~~~~~~~^ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h: In function 'void get_seqID(const std::string&, const std::string&, std::string&, double&, int&)': -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:458:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 458 | for (int i=0;i struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -8114,19 +8311,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/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)': -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:697:14: warning: statement has no effect [-Wunused-value] - 697 | for (i;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 878 | for (i=0;i struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h: In function 'void output_pymol(std::string, std::string, std::string, double*, double (*)[3], int, int, int, int, const char*, const char*, const char*, const std::vector >&, const std::vector >&, std::string, std::string)': -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:1604:38: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'std::map, int>::mapped_type' {aka 'int'} [-Wsign-compare] - 1604 | if (atom_site_pos==_atom_site["Cartn_x"]) -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:1607:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'std::map, int>::mapped_type' {aka 'int'} [-Wsign-compare] - 1607 | else if (atom_site_pos==_atom_site["Cartn_y"]) -/build/reproducible-path/openstructure-2.5.0/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"]) 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, @@ -8161,28 +8338,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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 struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -8197,16 +8352,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:2162:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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-2.5.0/modules/bindings/src/USalign/TMalign.h:3289:12: warning: variable 'Lnorm_d0' set but not used [-Wunused-but-set-variable] - 3289 | double Lnorm_d0; - | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -8215,14 +8360,19 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.cc:21: + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/impl/align_impl.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/local_align.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/seq/alg/src/entropy.hh:22: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -8232,10 +8382,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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 struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:3572:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::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-2.5.0/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 struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -8293,6 +8420,12 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/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] @@ -8301,40 +8434,30 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.cc:24: -/build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h: In function 'double homo_refined_greedy_search(double**, int*, int*, int, int, double**, double**, double, int, double**)': -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:440:12: warning: unused variable 'TMnow' [-Wunused-variable] - 440 | double TMnow =0; - | ^~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:441:12: warning: unused variable 'TMmax' [-Wunused-variable] - 441 | double TMmax =0; - | ^~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h: In function 'void clear_full_PDB_lines(std::vector > >, std::string)': -/build/reproducible-path/openstructure-2.5.0/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 struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -8343,54 +8466,28 @@ 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/local_align.cc:19: + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/modules/bindings/src/USalign/MMalign.h: In function 'void output_dock(const std::vector >&, int, int, int, std::string, int, double**, const std::string&)': -/build/reproducible-path/openstructure-2.5.0/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 struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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-2.5.0/modules/bindings/src/USalign/MMalign.h: In function 'int copy_chain_pair_data(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, std::vector > >&, std::vector > >&, int*, int*, std::vector >&)': -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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 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-2.5.0/modules/bindings/src/USalign/MMalign.h: In function 'void writeTrimComplex(std::vector > >&, std::vector >&, std::vector&, std::vector >&, std::vector&, const std::string&, std::string)': -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: + 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-2.5.0/modules/bindings/src/USalign/param_set.h:6, + from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:6: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8426,12 +8525,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/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/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:23: + 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-2.5.0/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 | ^~~~~~~~ @@ -8492,6 +8589,14 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -8500,19 +8605,17 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/merge_pairwise_alignments.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/merge_pairwise_alignments.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/hmm_score.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/hmm_score.cc:1: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/seq/alg/src/merge_pairwise_alignments.cc:21: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/profile_handle.hh:27, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -8522,6 +8625,14 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -8532,7 +8643,7 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/ins_del.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/sequence_similarity.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -8557,31 +8668,12 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:27: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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 - | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -8626,18 +8708,15 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/bindings/wrap_tmalign.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:25: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh: At global scope: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/contact_prediction_score.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/bindings/src/USalign/param_set.h:6, - from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:6: + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -8647,6 +8726,24 @@ /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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/distance_map.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/distance_map.cc:25: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -8655,15 +8752,19 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/contact_prediction_score.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/impl/align_impl.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/global_align.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -8681,18 +8782,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/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_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o -MF CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o.d -o CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/hmm_pseudo_counts.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: -/build/reproducible-path/openstructure-2.5.0/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 - | ^~~~~~~~ -[ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/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_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/src/CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -MF CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o.d -o CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/hmm_score.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, @@ -8768,66 +8857,29 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/variance_map.cc:29: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/distance_map.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/variance_map.cc:31: -/build/reproducible-path/openstructure-2.5.0/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 - | ^~~~~~~~ [ 25%] Linking CXX shared library ../../../stage/lib/libost_db.so cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0=. -fstack-protector-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.2.5 -o ../../../stage/lib/libost_db.so.2.5.0 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-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /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 /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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/hmm_score.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/hmm_score.cc:1: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/info/pymod/wrap_info.cc:29: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/profile_handle.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/hmm_score.hh:23: + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -8837,14 +8889,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_db.so.2.5.0 ../../../stage/lib/libost_db.so.2.5 ../../../stage/lib/libost_db.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 25%] Built target ost_db @@ -8854,53 +8898,46 @@ make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu' -[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/processor.cc.o [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/amino_acids.cc.o +[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib_base.cc.o +[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/processor.cc.o [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/conop.cc.o +[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/heuristic.cc.o [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o -[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib_base.cc.o +[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/diag.cc.o +[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/rule_based.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/conop/src/compound_lib_base.cc +[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o +[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/processor.cc.o -MF CMakeFiles/ost_conop.dir/processor.cc.o.d -o CMakeFiles/ost_conop.dir/processor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/processor.cc cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/conop/src/amino_acids.cc +[ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o +[ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/ring_finder.cc.o cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/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-2.5.0/modules/conop/src/conop.cc cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/conop/src/minimal_compound_lib.cc -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/conop/src/compound_lib_base.cc -[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/heuristic.cc.o cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/conop/src/heuristic.cc -[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/diag.cc.o -[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/rule_based.cc.o -[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/diag.cc.o -MF CMakeFiles/ost_conop.dir/diag.cc.o.d -o CMakeFiles/ost_conop.dir/diag.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/diag.cc -[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/ring_finder.cc.o -[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/conop/src/rule_based.cc cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/conop/src/model_check.cc -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/conop/src/ring_finder.cc -[ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/conop/src/compound.cc cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/conop/src/compound_lib.cc -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/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) - | ^~~~~~~~~ +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/conop/src/ring_finder.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/amino_acids.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/amino_acids.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/rule_based.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/conop/src/amino_acids.hh:24: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -8910,28 +8947,22 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/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/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib_base.hh:4: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -8945,7 +8976,7 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/rule_based.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/processor.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -8956,7 +8987,7 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/rule_based.cc:20: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -8971,9 +9002,9 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/diag.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/diag.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/model_check.hh:4, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/model_check.cc:1: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -8982,8 +9013,7 @@ from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/diag.hh:22: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -8996,19 +9026,21 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/heuristic.cc:22: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/diag.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/diag.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/heuristic.cc:20: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -9018,28 +9050,10 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/processor.cc:21: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/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-2.5.0/modules/conop/src/model_check.cc:2: +/build/reproducible-path/openstructure-2.5.0/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/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: +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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -9102,7 +9115,8 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib_base.hh:5, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib_base.cc:1: + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/minimal_compound_lib.hh:5, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/minimal_compound_lib.cc:1: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -9119,10 +9133,27 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/model_check.cc:2: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9131,17 +9162,16 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/conop.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib_base.hh:5, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib_base.cc:1: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/conop.cc:19: +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-2.5.0/modules/conop/src/compound.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -9151,6 +9181,12 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -11381,7 +10834,8 @@ from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/structure_analysis.cc:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -11391,22 +10845,23 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/gfx/src/impl/connect_renderer_base.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/consistency_checks.cc:21: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/consistency_checks.cc:20: +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-2.5.0/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 | ^~~~~~~~ @@ -11416,15 +10871,11 @@ /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/color_ops/entity_view_color_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/gfx/src/color_ops/entity_view_color_op.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/uniform_color_op.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11435,33 +10886,8 @@ 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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.hh:37, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gost_exporter.cc:27: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/modules/gfx/src/gost_exporter.cc:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/dyn_cast.hh:22, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -11471,47 +10897,27 @@ /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_peak.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/pymod/export_peak.cc +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-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.cc:21: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/color_op.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:22: +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-2.5.0/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 | ^~~~~~~~ @@ -11521,52 +10927,18 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.cc:22: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.cc:23: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/pdbize.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/pdbize.cc:19: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu' +[ 34%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/base/pymod/export_atom.cc +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-2.5.0/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/uniform_color_op.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_level_color_op.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11578,7 +10950,7 @@ from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/dyn_cast.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/uniform_color_op.cc:20: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -11588,26 +10960,15 @@ /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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/pdbize.hh:25: -/build/reproducible-path/openstructure-2.5.0/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 - | ^~~~~~~~ -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/gfx/src/color_ops/basic_gradient_color_op.cc -[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/adjacency_bitmap.cc.o -MF CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o.d -o CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/adjacency_bitmap.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_color_op.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/entity_view_color_op.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11623,15 +10984,12 @@ /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/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/alg/src/contact_overlap.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/gfx/src/color_ops/gradient_level_color_op.cc +[ 34%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/entity_view_color_op.cc:21: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_color_op.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11647,48 +11005,9 @@ /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/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/alg/src/domain_find.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/gfx/src/impl/entity_renderer.cc -[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/similarity_matrix.cc.o -MF CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o.d -o CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/similarity_matrix.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/gfx/src/impl/entity_detail.cc -[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/alg/src/accessibility.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/gfx/src/impl/cartoon_renderer.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/gfx/src/impl/custom_renderer.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/adjacency_bitmap.cc:19: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_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/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/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-2.5.0/modules/mol/alg/src/sec_struct.cc +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/pymod/export_data.cc +[ 34%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/pymod/export_data_algorithm.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11714,24 +11033,26 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/adjacency_bitmap.hh:9, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/adjacency_bitmap.cc:24: -/build/reproducible-path/openstructure-2.5.0/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 - | ^~~~~~~~ +[ 34%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/pymod/export_extent.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.cc:23: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/similarity_matrix.hh:7, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/similarity_matrix.cc:1: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/dft.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/entity_to_density.cc:10: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11741,8 +11062,8 @@ 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-2.5.0/modules/mol/alg/src/similarity_matrix.hh:5: + from /usr/include/c++/13/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -11752,76 +11073,126 @@ /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/impl/cpk_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/gfx/src/impl/cpk_renderer.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/gfx/src/impl/debug_renderer.cc -[ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/gfx/src/impl/simple_renderer.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/surface.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/basic_gradient_color_op.cc:22: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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); - | ^~~~~ +[ 34%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/pymod/export_image_handle.cc +[ 34%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/img/base/pymod/export_peak.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-2.5.0/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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:34, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_base.hh:25, + from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/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-2.5.0/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 file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc:2: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/color_op.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.cc:22: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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 /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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_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/alg/src/CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/alg/src/nonstandard.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc:3: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_level_color_op.cc:22: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/dyn_cast.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_level_color_op.cc:20: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -11831,6 +11202,8 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/gfx/src/impl/trace_renderer_base.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11854,71 +11227,26 @@ /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/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/alg/src/molck.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/surface.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/basic_gradient_color_op.cc:22: +/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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); + | ^~~~~ +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o +cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/gfx/src/impl/mapped_property.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:1: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_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/sline_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/gfx/src/impl/sline_renderer.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_detail.cc:22: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_view.hh:25, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_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/line_trace_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/gfx/src/impl/line_trace_renderer.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/view_op.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_renderer.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11926,8 +11254,7 @@ from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_renderer.cc:23: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -11962,138 +11289,25 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 35%] Linking CXX shared library ../../../stage/lib/libost_bindings.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_bindings.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-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.2.5 -o ../../../stage/lib/libost_bindings.so.2.5.0 CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /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 /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 In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/peak.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_peak.cc:29: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_detail.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc:1: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/domain_find.cc:3: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.cc:19: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_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/alg/src/CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -cd /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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-2.5.0/modules/mol/alg/src/find_membrane.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/domain_find.cc:9: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/nonstandard.cc:27: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/nonstandard.cc:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_view.hh:25, + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -12135,32 +11349,11 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/molck.cc:1: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/view_op.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_renderer.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -12169,7 +11362,7 @@ from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:24: + from /build/reproducible-path/openstructure-2.5.0/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 | ^~~~~~~~ @@ -12187,92 +11380,6 @@ /build/reproducible-path/openstructure-2.5.0/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-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38: -/build/reproducible-path/openstructure-2.5.0/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-2.5.0/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-2.5.0/modules/mol/alg/src/molck.cc:4: -/build/reproducible-path/openstructure-2.5.0/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