Diff of the two buildlogs: -- --- b1/build.log 2024-08-21 05:26:10.298859919 +0000 +++ b2/build.log 2024-08-21 05:42:51.568330846 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Aug 20 17:14:29 -12 2024 -I: pbuilder-time-stamp: 1724217269 +I: Current time: Wed Sep 24 01:49:31 +14 2025 +I: pbuilder-time-stamp: 1758628171 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -34,51 +34,83 @@ dpkg-source: info: applying 15a499485ede152b6d432b7c91f1084e9e11bd8f.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3151746/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1885813/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-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 Sep 23 11:49 /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/1885813/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1885813/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' + 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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(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=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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='6b6506ea7ce748e5ac5410fc22b9bea1' - 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='3151746' - PS1='# ' - PS2='> ' + INVOCATION_ID=62d3071659a64fbca10c3f0083c3181f + 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=1885813 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.nHTQYAWA/pbuilderrc_PtiW --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.nHTQYAWA/b1 --logfile b1/build.log openstructure_2.5.0-3.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.nHTQYAWA/pbuilderrc_6IJy --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.nHTQYAWA/b2 --logfile b2/build.log openstructure_2.5.0-3.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.1.0-23-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.99-1 (2024-07-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.9.7+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1~bpo12+1 (2024-07-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3151746/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1885813/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -615,7 +647,7 @@ Get: 455 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5.sip amd64 12.15.0-1 [56.6 kB] Get: 456 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5 amd64 5.15.11+dfsg-1 [2515 kB] Get: 457 http://deb.debian.org/debian unstable/main amd64 voronota amd64 1.22.3149-2 [2057 kB] -Fetched 327 MB in 5s (65.5 MB/s) +Fetched 327 MB in 10s (34.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19730 files and directories currently installed.) @@ -2085,8 +2117,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Aug 21 05:18:31 UTC 2024. -Universal Time is now: Wed Aug 21 05:18:31 UTC 2024. +Local time is now: Tue Sep 23 11:53:58 UTC 2025. +Universal Time is now: Tue Sep 23 11:53:58 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-3.1) ... @@ -2482,7 +2514,11 @@ 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_2.5.0-3_source.changes +I: user script /srv/workspace/pbuilder/1885813/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1885813/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_2.5.0-3_source.changes dpkg-buildpackage: info: source package openstructure dpkg-buildpackage: info: source version 2.5.0-3 dpkg-buildpackage: info: source distribution unstable @@ -2634,8 +2670,8 @@ Static Libraries (-DENABLE_STATIC) : OFF Debian/Ubuntu directory layout (-DUBUNTU_LAYOUT) : ON Hidden object visibility (-DHIDDEN_VISIBILITY) : OFF --- Configuring done (1.4s) --- Generating done (0.4s) +-- Configuring done (2.4s) +-- Generating done (0.6s) CMake Warning: Manually-specified variables were not used by the project: @@ -2660,1194 +2696,1183 @@ make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/depend make -f modules/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.py.dir/depend make -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 -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/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/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 -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' 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/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/depend +make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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=" +make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/depend +make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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 -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' -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/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=" 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[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_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/depend +make -f modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/depend make[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=" -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/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=" +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[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/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/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[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[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[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/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]: 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]: 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/python3.12/dist-packages//ost/bindings/./__init__.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/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/conop/./__init__.py +make -f modules/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.py.dir/build +make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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/build -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/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/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/python3.12/dist-packages//ost/db/./__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' +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 +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 -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build +make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/build +make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build make[3]: 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/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.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/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 -f modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build.make modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build +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/python3.12/dist-packages//ost/bindings/./__init__.py +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/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -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/python3.12/dist-packages//ost/conop/./__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[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/python3.12/dist-packages//ost/gui/scene/__init__.py +make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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/python3.12/dist-packages//ost/geom/./__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/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/python3.12/dist-packages//ost/bindings/./lga.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/python3.12/dist-packages//ost/gfx/./__init__.py -make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.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' -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[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 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/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/python3.12/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/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[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/python3.12/dist-packages//ost/gui/./__init__.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/python3.12/dist-packages//ost/conop/./cleanup.py make[3]: Leaving 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/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/python3.12/dist-packages//ost/db/./__init__.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/python3.12/dist-packages//ost/bindings/./lga.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_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/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' -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/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/python3.12/dist-packages//ost/conop/./cleanup.py make[3]: Leaving 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/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/python3.12/dist-packages//ost/bindings/./hbplus.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/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/python3.12/dist-packages//ost/gfx/./py_gfx_obj.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/scene/__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/__init__.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/python3.12/dist-packages//ost/gui/dng/termuse.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' -[ 0%] Built target subst___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 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/./init_context_menu.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_context_menu.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/python3.12/dist-packages//ost/gui/dng/termuse.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/python3.12/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/python3.12/dist-packages//ost/gui/scene/color_select_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/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/python3.12/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/dng/superpositiondialog.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/superpositiondialog.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/openstructure/libexec 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 subst___init__.py make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/depend make[3]: 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=" +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/python3.12/dist-packages//ost/bindings/./msms.py +[ 0%] Built target ost_db_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/combo_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/combo_options_widget.py [ 0%] Built target ost_geom_pymod make -f modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build.make modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/depend -cd /build/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/python3.12/dist-packages//ost/gui/scene/color_options_widget.py +[ 0%] Built target gui_images +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/python3.12/dist-packages//ost/gui/./init_menubar.py +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/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=" +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/python3.12/dist-packages//ost/gui/dng/init.py +[ 0%] Built target ost_gfx_pymod +make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/depend [ 0%] Built target ost_conop_pymod -[ 0%] Built target gui_images -make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.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/./init_menubar.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_menubar.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/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=" -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 -make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/depend -[ 0%] Built target ost_gfx_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/delete_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/delete_icon.png -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/python3.12/dist-packages//ost/bindings/./tmtools.py -[ 0%] Built target ost_db_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/dng/superpositiondialog.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/superpositiondialog.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/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/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build 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/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/python3.12/dist-packages//ost/img/./__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/tests 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=" +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/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/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/python3.12/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/color_select_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/color_select_widget.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/distance_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/distance_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/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/python3.12/dist-packages//ost/bindings/./tmtools.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/python3.12/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/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/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.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/dng/menu.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/menu.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/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/python3.12/dist-packages//ost/info/./__init__.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/./dssp.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./dssp.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]: 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/./init_spacenav.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_spacenav.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 -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/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/python3.12/dist-packages//ost/gui/scene/combo_options_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/dng/init.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/init.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_splash.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_splash.py +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/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/python3.12/dist-packages//ost/img/alg/./__init__.py +make[3]: Leaving 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/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/python3.12/dist-packages//ost/img/./__init__.py +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' 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/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 -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' 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/python3.12/dist-packages//ost/io/./__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/python3.12/dist-packages//ost/info/./__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/distance_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/distance_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/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/python3.12/dist-packages//ost/bindings/./dssp.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/custom_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/custom_widget.py +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build +make[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/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/python3.12/dist-packages//ost/mol/./__init__.py -[ 0%] Built target create_stage 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]: 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/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/python3.12/dist-packages//ost/mol/alg/./__init__.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_splash.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_splash.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/python3.12/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/scene/gradient_editor_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_editor_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/./remote.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/io/./remote.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/find_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/find_icon.png +[ 0%] Built target ost_gui_dng_pymod +make[3]: Leaving 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 -[ 0%] Built target ost_img_pymod +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 0%] Built target create_stage 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/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=" -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/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/python3.12/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/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/python3.12/dist-packages//ost/gui/dng/menu.py 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/seq/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/seq/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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/cpk_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/cpk_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/./trajectory_viewer.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./trajectory_viewer.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_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_info_handler.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/./utils.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./utils.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/map_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/map_icon.png -[ 0%] Built target ost_info_pymod -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/python3.12/dist-packages//ost/io/./remote.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/custom_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/custom_widget.py -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/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/python3.12/dist-packages//ost/mol/alg/./views.py -[ 0%] Built target ost_mol_pymod -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 -f modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build.make modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build -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/python3.12/dist-packages//ost/bindings/./naccess.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/menubar_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/menubar_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/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/python3.12/dist-packages//ost/mol/mm/./__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/./repository.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/io/./repository.py +[ 0%] Built target ost_img_pymod make -f modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build.make modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/depend +cd /build/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/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/python3.12/dist-packages//ost/seq/./__init__.py -make[3]: Entering 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/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/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/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/python3.12/dist-packages//ost/gui/./helpwidget.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/python3.12/dist-packages//ost/io/./repository.py +[ 0%] Built target ost_info_pymod +[ 0%] Built target ost_img_alg_pymod +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[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=" -[ 0%] Built target ost_img_alg_pymod +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=" 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/python3.12/dist-packages//ost/mol/alg/./superpose.py -make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.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/scene/gradient_editor_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_editor_widget.py -[ 0%] Built target ost_gui_dng_pymod -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/python3.12/dist-packages//ost/mol/mm/./antechamber.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/./hhblits.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/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/gradient_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_list_model.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/./naccess.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./naccess.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/./helpwidget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./helpwidget.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]: 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 -f modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build.make modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_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/./table.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./table.py +[ 0%] Built target ost_mol_pymod 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 -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 -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/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/python3.12/dist-packages//ost/seq/alg/./__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/./qsscoring.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./qsscoring.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/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/mm/./__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_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.12.5 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/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/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 make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.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/./hhblits2.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hhblits2.py +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[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/python3.12/dist-packages//ost/seq/./__init__.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/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/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/python3.12/dist-packages//ost/seq/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/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/python3.12/dist-packages//ost/gui/scene/gradient_info_handler.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/./gosty_startup.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./gosty_startup.py +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_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.12.5 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/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' make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_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/gradient_preset_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_preset_widget.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/./qsscoring.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./qsscoring.py +[ 0%] Built target ost_io_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/./table.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./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/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=3.12.5 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/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/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 -[ 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/scene/gradient_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_list_model.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/./hhblits3.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hhblits3.py -[ 0%] Built target ost_io_pymod make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend -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/./trajectory_analysis.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./trajectory_analysis.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/python3.12/dist-packages//ost/seq/alg/./mat.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/./hhblits.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hhblits.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/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]: 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/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/python3.12/dist-packages//ost/mol/mm/./antechamber.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/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/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/python3.12/dist-packages//ost/seq/alg/./mat.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/./gosty_startup.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./gosty_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/hsc_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/hsc_widget.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/./trajectory_analysis.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./trajectory_analysis.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 scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build [ 0%] Built target ost_seq_pymod make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend 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/./hhblits2.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hhblits2.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=3.12.5 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/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 && /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=" -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/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/python3.12/dist-packages//ost/gui/scene/gradient_preset_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/./blast.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./blast.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 && /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=" make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.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/./structure_analysis.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./structure_analysis.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/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 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=3.12.5 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/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/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/python3.12/dist-packages//ost/seq/alg/./renumber.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.in -DOUT_FILE=ost -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.12.5 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/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/immutable_gradient_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/immutable_gradient_info_handler.py +cd /build/reproducible-path/openstructure-2.5.0/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/python3.12/dist-packages//ost/mol/alg/./structure_analysis.py +[ 0%] Built target subst_ost_config 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 -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=3.12.5 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/dist-packages/ -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake -[ 0%] Built target ost_gui_pymod -[ 0%] Built target subst_ost_startup.py 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 +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/python3.12/dist-packages//ost/bindings/./hhblits3.py +[ 0%] Built target ost_mol_mm_pymod make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/depend +[ 0%] Built target subst_ost_startup.py +make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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 -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/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/python3.12/dist-packages//ost/gui/scene/hsc_widget.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/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/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 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/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/python3.12/dist-packages//ost/bindings/./cadscore.py -[ 0%] Built target subst_ost_config -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/python3.12/dist-packages//ost/mol/alg/./helix_kinks.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/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/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend 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/python3.12/dist-packages//ost/seq/alg/./aaindex.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/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=" -make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_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/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[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 0%] Built target ost_gui_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/immutable_preset_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/immutable_preset_info_handler.py +make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_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/ost_base_pymod.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/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/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 -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/python3.12/dist-packages//ost/gui/scene/immutable_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/./helix_kinks.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./helix_kinks.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/./blast.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./blast.py 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 -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/python3.12/dist-packages//ost/bindings/./kclust.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/python3.12/dist-packages//ost/mol/alg/./hbond.py +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]: 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/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 +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 [ 0%] Built target subst_ost +[ 0%] Built target subst_dng +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/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 +make[3]: Entering 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/depend 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/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/build +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[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/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]: 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=" +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/python3.12/dist-packages//ost/mol/alg/./hbond.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/init_inspector.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/init_inspector.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/./base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./base.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build -cd /build/reproducible-path/openstructure-2.5.0/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 -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/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 -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/python3.12/dist-packages//ost/./settings.py 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]: 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/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/build -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/python3.12/dist-packages//ost/bindings/./ialign.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/immutable_preset_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/immutable_preset_info_handler.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/./settings.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./settings.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/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 -[ 0%] Built target subst_dng -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 -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/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/python3.12/dist-packages//ost/mol/alg/./lddt.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/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 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 -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=" -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/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/python3.12/dist-packages//ost/bindings/./cadscore.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/./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/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/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/python3.12/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/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/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/python3.12/dist-packages//ost/bindings/./mmseqs2.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/./stutil.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/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/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]: 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/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_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/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/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/python3.12/dist-packages//ost/gui/scene/inspector_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/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/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/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/python3.12/dist-packages//ost/./stutil.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/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/python3.12/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/init_inspector.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/init_inspector.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/./kclust.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./kclust.py 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 -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/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/python3.12/dist-packages//ost/./table.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/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/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/python3.12/dist-packages//ost/mol/alg/./qsscore.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/split_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/split_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/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 +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/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/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/./dockq.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./dockq.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/map_level_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/map_level_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 /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/python3.12/dist-packages//ost/./table.py [ 0%] Built target actions -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/python3.12/dist-packages//ost/mol/alg/./scoring.py -make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/depend -cd /build/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/python3.12/dist-packages//ost/gui/scene/inspector_widget.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/./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/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/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 -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/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 +make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/depend +cd /build/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/python3.12/dist-packages//ost/mol/alg/./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/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 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=" +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/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/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 +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/python3.12/dist-packages//ost/bindings/./ialign.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 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/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/python3.12/dist-packages//ost/mol/alg/./chain_mapping.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/python3.12/dist-packages//ost/./table_selector.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/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/python3.12/dist-packages//ost/gui/scene/preset.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/./mat.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat.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/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/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/python3.12/dist-packages//ost/mol/alg/./chain_mapping.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 +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/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/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/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/python3.12/dist-packages//ost/./xmlrunner.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_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl.hh [ 0%] Built target ost_seq_alg_pymod +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/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/python3.12/dist-packages//ost/gui/scene/remote.py make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/depend -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 -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/./stereochemistry.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./stereochemistry.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/map_level_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/map_level_widget.py -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]: 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[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 +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/python3.12/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/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 +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_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_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/./integrity_error.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./integrity_error.hh -[ 0%] Built target ost_bindings_pymod -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/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=" -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/python3.12/dist-packages//ost/./xmlrunner.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/./testutils.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./testutils.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/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]: 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/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/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/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/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=" +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/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/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/python3.12/dist-packages//ost/mol/alg/./ligand_scoring.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/preset.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset.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/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[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/preset_editor_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_editor_list_model.py make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_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/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 -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/./mat3.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat3.hh -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/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/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/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/python3.12/dist-packages//ost/bindings/./dockq.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/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/python3.12/dist-packages//ost/__init__.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/./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/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/python3.12/dist-packages//ost/mol/alg/./dockq.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_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_handle.hh [ 0%] Built target ost_config_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/preset_editor_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_editor_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/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/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/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 -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/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/python3.12/dist-packages//ost/./testutils.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/depend +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 && /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[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/./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' -make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_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/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[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 -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/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/python3.12/dist-packages//ost/gui/scene/remote.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/./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/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/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/python3.12/dist-packages//ost/mol/alg/./dockq.py +[ 0%] Built target scene_icons +make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/depend +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 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/./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/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/python3.12/dist-packages//ost/__init__.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/./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/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 -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_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/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]: 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/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 && /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=" +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 [ 0%] Built target ost_bindings_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/preset_editor_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_editor_list_model.py -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/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/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 +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/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/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/python3.12/dist-packages//ost/gui/scene/preset_info_handler.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/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=" +[ 0%] Built target ost_bindings_pymod +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/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 +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' +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 && /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/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/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/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/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/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 -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/./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/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/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/python3.12/dist-packages//ost/gui/scene/preset_editor_widget.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_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_group.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/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 [ 0%] Built target ost_base_pymod -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_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/build 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/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/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=" -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/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/python3.12/dist-packages//ost/gui/scene/preset_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/./conop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./conop.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_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/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 +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/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 +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/preset_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_list_model.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/./sqlite_wrap.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_wrap.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/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_mol_alg_pymod -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 +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/depend -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/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 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/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/build 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/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/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/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/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/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/python3.12/dist-packages//ost/gui/scene/preset_list_model.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/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 -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build +make[3]: Entering 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 +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/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/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 -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/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/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/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/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/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/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/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/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/python3.12/dist-packages//ost/gui/scene/preset_widget.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/./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/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/./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/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/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/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/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]: 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 -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/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 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 -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/python3.12/dist-packages//ost/gui/scene/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/./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/./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/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/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/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/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/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/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/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/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/python3.12/dist-packages//ost/gui/scene/render_mode_widget.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 -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/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/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/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/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/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/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/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/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/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/python3.12/dist-packages//ost/gui/scene/render_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/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/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/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/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/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/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/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/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/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 -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.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/python3.12/dist-packages//ost/gui/scene/render_op.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/./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/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/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_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/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/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/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/./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/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/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/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/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/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/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/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/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/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/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/python3.12/dist-packages//ost/gui/scene/render_options_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/./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/./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/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/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/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/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 -[ 0%] Built target ost_db_headers -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/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/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 -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/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/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/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/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/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/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/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 -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/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/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/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/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/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 +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_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/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/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/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/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/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/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/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/python3.12/dist-packages//ost/gui/scene/scene_observer_impl.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/./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/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/./item_type.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./item_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_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/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/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/./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/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 +[ 0%] Built target ost_seq_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/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 +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/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/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 +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/./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/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/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/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_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/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/./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/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 make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build 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/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/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/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/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/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/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/scene_selection_helper.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/scene_selection_helper.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/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/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/./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/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/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/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/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/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/python3.12/dist-packages//ost/gui/scene/scene_selection_helper.py +[ 0%] Built target ost_db_headers +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 && /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=" +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/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/./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/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/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/python3.12/dist-packages//ost/gui/scene/simple_widget.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/./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/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/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/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/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/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/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/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/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/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/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/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/python3.12/dist-packages//ost/gui/scene/sline_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_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/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 +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/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/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/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/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/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/python3.12/dist-packages//ost/gui/scene/simple_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/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 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/./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/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/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/./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/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/python3.12/dist-packages//ost/gui/scene/toolbar_options_widget.py +make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build +cd /build/reproducible-path/openstructure-2.5.0/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 +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 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_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/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/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/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/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/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 -[ 0%] Built target ost_conop_headers -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/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/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/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/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/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/python3.12/dist-packages//ost/gui/scene/trace_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_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 -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 && /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=" +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/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/./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/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_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/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 -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/./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/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/./string_ref.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./string_ref.hh -[ 0%] Built target ost_seq_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/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/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/python3.12/dist-packages//ost/gui/scene/sline_widget.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/./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/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 +[ 0%] Built target ost_info_headers make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/depend -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 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=" -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/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/python3.12/dist-packages//ost/gui/scene/tube_widget.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/./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/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/./fixed_string.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./fixed_string.hh 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 -[ 0%] Built target ost_info_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/./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/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.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/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 -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/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/python3.12/dist-packages//ost/gui/scene/uniform_color_widget.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/./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/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/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/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/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/./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/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/python3.12/dist-packages//ost/gui/scene/toolbar_options_widget.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/./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/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 +[ 0%] Built target ost_conop_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/./tri_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./tri_matrix.hh make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/depend -cd /build/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 +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 && /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/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 -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/impl/query_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_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/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/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/./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/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/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/python3.12/dist-packages//ost/gui/scene/trace_widget.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/./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/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 -make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/build -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/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/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/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/./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/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/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 -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/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/python3.12/dist-packages//ost/gui/scene/visibility_op.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/./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/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/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/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_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/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/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 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/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/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/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/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/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/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/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/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 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/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/tube_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/tube_widget.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/./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/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/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/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/./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/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/python3.12/dist-packages//ost/gui/scene/line_trace_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_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/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/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/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/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/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/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/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/python3.12/dist-packages//ost/gui/scene/uniform_color_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/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/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/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/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/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/./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/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/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/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/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/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/python3.12/dist-packages//ost/gui/scene/wireframe_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/./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_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/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/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/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/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/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/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/./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/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/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/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/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/python3.12/dist-packages//ost/gui/scene/query_editor.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/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/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/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/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/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/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/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/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/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/octree_isocont.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.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/./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/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/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 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/./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/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/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/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/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/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/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/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/python3.12/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/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/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/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/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/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/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/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/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/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/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/python3.12/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/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/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 [ 0%] Built target ost_base_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/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/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/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/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 make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend -[ 0%] Built target ost_gui_scene_pymod 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/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/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/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/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/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/python3.12/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/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/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/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/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/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/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/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/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 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/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/./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/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/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/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/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/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/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/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/./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/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/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/python3.12/dist-packages//ost/gui/scene/query_editor.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_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/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 +[ 0%] Built target ost_geom_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/debug_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.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/./histogram.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./histogram.hh make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build 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' -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/./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/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/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/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/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/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/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/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/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/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 -[ 0%] Built target ost_config +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 +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/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/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/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 -[ 0%] Built target ost_geom_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/./data_algorithm.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./data_algorithm.hh -[ 0%] Built target ost_seq_alg_headers +[ 0%] Built target ost_config 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/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/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/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 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/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/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/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/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/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/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/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 +[ 0%] Built target ost_gui_scene_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/./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/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/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/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/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/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 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/mol/surface_io_msms_handler.hh 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/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/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 -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/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/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/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/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 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/./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/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/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 -[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat2.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/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/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/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/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 -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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/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/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/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/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/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/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/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./data.hh 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/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 [ 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/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/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 +[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat4.cc.o +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/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 +[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat2.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 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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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 +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/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/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 -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/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/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/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 +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/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/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/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/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/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/./bond_table.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_table.hh +[ 0%] Built target ost_seq_alg_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/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/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/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/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/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/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/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/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/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/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 +[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vec3.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/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/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/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/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/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/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/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_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/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/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/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/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/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 +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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/./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/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/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/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/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/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/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_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/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/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/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/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_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 -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/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/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/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/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/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/./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/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/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/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/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/./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/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/./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/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 +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/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/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/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/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/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 -[ 0%] Built target ost_mol_alg_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/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/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 +[ 0%] Built target ost_mol_mm_headers +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/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/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/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/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/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/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/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/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/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 +[ 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/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/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/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/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 +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/./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/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/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_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle.hh +[ 0%] Built target ost_mol_alg_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/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 -[ 0%] Built target ost_mol_mm_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/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/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_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/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/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/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 -[ 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/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/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/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/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/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/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 [ 0%] 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/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/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/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 +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/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/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/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/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/./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/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/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/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/custom_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/custom_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_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/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/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/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/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/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/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/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/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/./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/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/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/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/./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/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/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/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/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/./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/./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/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/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/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/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/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/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/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/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/./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/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/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/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/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/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/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/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/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/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/./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/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/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/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/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/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/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/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 -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/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/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/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/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 +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/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_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/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/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/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 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_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_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/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/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/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_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/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/./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/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/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/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/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 /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/./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_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/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/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_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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 /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/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/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/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/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/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/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/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/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/./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/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/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_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/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/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/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/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/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/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/./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/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/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/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/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_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/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/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/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/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/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/./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/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/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/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/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/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/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/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/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 -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/./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/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/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/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/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/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/./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/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/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/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 -[ 0%] Built target ost_img_alg_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/./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/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/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 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 -[ 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/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/./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/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/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/./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/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/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/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/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/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/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/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/./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/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/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/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/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/./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/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/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/./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/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/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/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/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/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/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/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_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/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/./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/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/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 +[ 0%] 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/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/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/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/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/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/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/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/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/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/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/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 +[ 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/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/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/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/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/./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/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/./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/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/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/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/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/./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/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/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/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/./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/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/./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/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/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/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/./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/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 -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/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/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/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/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/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/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/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/./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/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/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/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_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/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/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/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_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/./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/./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/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/./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/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/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/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/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/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/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/./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/./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/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/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/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/./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/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/./gfx.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx.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/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/./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/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/./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/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_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/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/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/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/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/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/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/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/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/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 +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/./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/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/./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/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/./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/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/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/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/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 +[ 1%] Built target ost_img_headers 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/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/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/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/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/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/./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/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/./view_type_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_type_fw.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/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 +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/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/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/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/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/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/button_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_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/./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/./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/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/./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_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/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/./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/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 -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/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/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/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/./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/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/./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/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/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/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/./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/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/./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/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 +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/./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/./converting_streams.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./converting_streams.hh +[ 1%] Built target ost_mol_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/./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/./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/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/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 -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/panels/event_button.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/event_button.hh +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3.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/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/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/./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/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/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/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/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/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/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/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 -[ 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/./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/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/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/./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/./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/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 -[ 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/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/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/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 -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/./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/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/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/./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/./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/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/./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/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/context_menu.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/context_menu.hh -[ 1%] Built target ost_mol_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/./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/./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/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/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/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/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/./texture.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./texture.hh -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3.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/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 -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2_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/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/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/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/./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/./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/./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/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/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 -[ 1%] 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/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 +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/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/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/./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/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/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/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/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/./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/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/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/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/./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/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/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/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/./glext_include.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glext_include.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/./render_mode.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_mode.hh -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/quat.cc.o +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2_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/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/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/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/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/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/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/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/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/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/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/./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/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/./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_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/log_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/log_reader.hh -[ 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/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/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/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/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/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/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 -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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 -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/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 +[ 1%] 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/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 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/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/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/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/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/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/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/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/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/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/./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/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/./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/./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/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/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/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 +[ 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/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/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 +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/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 +[ 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/./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/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/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/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/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/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/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/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 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 | ^~~~~~~~ +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 In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, @@ -3862,32 +3887,71 @@ /usr/include/c++/14/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/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/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/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/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/./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/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/./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/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/./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/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/./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/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/./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/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/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 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/./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/./file_type_dialog.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_type_dialog.hh +[ 1%] Built target ost_gfx_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/./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/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 [ 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/./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 -[ 1%] Built target ost_gfx_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/./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/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/./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/./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/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/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/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/./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/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/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/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/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/./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/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/./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/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/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/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/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/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/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/./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/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 [ 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/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/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/./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/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/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_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/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/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/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/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/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/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/./file_viewer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_viewer.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 1%] Built target ost_io_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/./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/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/./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_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/./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/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/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/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/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/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/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/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/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./thin_splitter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./thin_splitter.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: @@ -3907,42 +3971,14 @@ /usr/include/c++/14/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/./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/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/./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/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/./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/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_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/./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_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/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_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_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/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/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/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/./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/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/./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/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./thin_splitter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./thin_splitter.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/./widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./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/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/./widget_geom_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_geom_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/./widget_pool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_pool.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/./widget_registry.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_registry.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/./widget_state_saver.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_state_saver.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_loader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_loader.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 make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 1%] Built target ost_gui_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/./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/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/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 -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 1%] Built target ost_io_headers [ 1%] Linking CXX shared library ../../../stage/lib/libost_geom.so cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_geom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_geom.so.2.5 -o ../../../stage/lib/libost_geom.so.2.5.0 CMakeFiles/ost_geom.dir/mat2.cc.o CMakeFiles/ost_geom.dir/mat3.cc.o CMakeFiles/ost_geom.dir/mat4.cc.o CMakeFiles/ost_geom.dir/vec3.cc.o CMakeFiles/ost_geom.dir/vecmat2_op.cc.o CMakeFiles/ost_geom.dir/vecmat3_op.cc.o CMakeFiles/ost_geom.dir/vecmat4_op.cc.o CMakeFiles/ost_geom.dir/composite2.cc.o CMakeFiles/ost_geom.dir/composite3.cc.o CMakeFiles/ost_geom.dir/composite2_op.cc.o CMakeFiles/ost_geom.dir/composite3_op.cc.o CMakeFiles/ost_geom.dir/quat.cc.o CMakeFiles/ost_geom.dir/transform.cc.o CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o CMakeFiles/ost_geom.dir/point_cloud.cc.o -L/build/reproducible-path/openstructure-2.5.0/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_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 @@ -3952,51 +3988,47 @@ make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/depend make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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.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.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/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.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' -[ 1%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/wrap_geom.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_vecmat4_op.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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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/wrap_geom.cc.o -MF CMakeFiles/_ost_geom.dir/wrap_geom.cc.o.d -o CMakeFiles/_ost_geom.dir/wrap_geom.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/wrap_geom.cc -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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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_vecmat2_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat2_op.cc -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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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 -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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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_vecmat4_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat4_op.cc [ 1%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat4.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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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_vec2.cc.o -[ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/generic_property.cc.o -[ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec4.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && 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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/base/src/CMakeFiles/ost_base.dir/log.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 -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/log.cc.o -MF CMakeFiles/ost_base.dir/log.cc.o.d -o CMakeFiles/ost_base.dir/log.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/log.cc -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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat3.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat3.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat3.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log_sink.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 -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/log_sink.cc.o -MF CMakeFiles/ost_base.dir/log_sink.cc.o.d -o CMakeFiles/ost_base.dir/log_sink.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/log_sink.cc -[ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/profile.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 -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/profile.cc.o -MF CMakeFiles/ost_base.dir/profile.cc.o.d -o CMakeFiles/ost_base.dir/profile.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/profile.cc -[ 2%] 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 -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/units.cc.o -MF CMakeFiles/ost_base.dir/units.cc.o.d -o CMakeFiles/ost_base.dir/units.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/units.cc -[ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/string_ref.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 -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/string_ref.cc.o -MF CMakeFiles/ost_base.dir/string_ref.cc.o.d -o CMakeFiles/ost_base.dir/string_ref.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/string_ref.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_vec2.cc:23: + 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 | ^~~~~~~~ @@ -4010,7 +4042,7 @@ 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_vec2.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4023,7 +4055,7 @@ 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_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 | ^~~~~~~~ @@ -4037,7 +4069,7 @@ 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_vecmat2_op.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4050,7 +4082,7 @@ 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_vec3.cc:22: + 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 | ^~~~~~~~ @@ -4064,7 +4096,7 @@ 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_vec3.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat3_op.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4074,12 +4106,10 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/platform.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 -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/platform.cc.o -MF CMakeFiles/ost_base.dir/platform.cc.o.d -o CMakeFiles/ost_base.dir/platform.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/platform.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_vecmat3_op.cc:22: + 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 | ^~~~~~~~ @@ -4093,7 +4123,7 @@ 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: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat4_op.cc:20: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4106,7 +4136,7 @@ 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_vecmat4_op.cc:23: + 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 | ^~~~~~~~ @@ -4120,7 +4150,7 @@ 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_vecmat4_op.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec4.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4133,7 +4163,7 @@ 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_vec4.cc:22: + 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 | ^~~~~~~~ @@ -4147,7 +4177,7 @@ 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_vec4.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat2.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4160,7 +4190,7 @@ 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/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 | ^~~~~~~~ @@ -4174,7 +4204,7 @@ 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/export_vec2.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4187,12 +4217,10 @@ 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/modules/geom/pymod/export_vecmat2_op.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 | ^~~~~~~~ -[ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/message.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 -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/message.cc.o -MF CMakeFiles/ost_base.dir/message.cc.o.d -o CMakeFiles/ost_base.dir/message.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/message.cc In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, @@ -4203,7 +4231,7 @@ 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/wrap_geom.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4213,8 +4241,35 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 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 -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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite2.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2.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: +/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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec3.cc:19: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/profile.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 -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/profile.cc.o -MF CMakeFiles/ost_base.dir/profile.cc.o.d -o CMakeFiles/ost_base.dir/profile.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/profile.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, @@ -4269,19 +4324,31 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/test_utils/compare_files.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 -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o -MF CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o.d -o CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/test_utils/compare_files.cc -[ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/boost_filesystem_helper.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 -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -MF CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o.d -o CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/boost_filesystem_helper.cc -[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o +[ 2%] 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 -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/units.cc.o -MF CMakeFiles/ost_base.dir/units.cc.o.d -o CMakeFiles/ost_base.dir/units.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/units.cc +[ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o +[ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/string_ref.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 -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/string_ref.cc.o -MF CMakeFiles/ost_base.dir/string_ref.cc.o.d -o CMakeFiles/ost_base.dir/string_ref.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/string_ref.cc 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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite3.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3.cc -[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o +[ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2_op.cc +[ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/platform.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 -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/platform.cc.o -MF CMakeFiles/ost_base.dir/platform.cc.o.d -o CMakeFiles/ost_base.dir/platform.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/platform.cc +[ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/message.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 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o -MF CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o.d -o CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/test_utils/compare_files.cc +[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3_op.cc +[ 5%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/boost_filesystem_helper.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 -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -MF CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o.d -o CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/boost_filesystem_helper.cc +[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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_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%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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_transform.cc.o -MF CMakeFiles/_ost_geom.dir/export_transform.cc.o.d -o CMakeFiles/_ost_geom.dir/export_transform.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_transform.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 CMakeFiles/ost_base.dir/units.cc.o CMakeFiles/ost_base.dir/string_ref.cc.o CMakeFiles/ost_base.dir/platform.cc.o CMakeFiles/ost_base.dir/message.cc.o CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -L/build/reproducible-path/openstructure-2.5.0/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_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 -[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3_op.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_base.so.2.5 ../../../stage/lib/libost_base.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 5%] Built target ost_base @@ -4291,18 +4358,18 @@ make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_impl.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_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/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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_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%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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_transform.cc.o -MF CMakeFiles/_ost_geom.dir/export_transform.cc.o.d -o CMakeFiles/_ost_geom.dir/export_transform.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_transform.cc [ 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_impl.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_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 +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 +[ 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_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_composite2.cc:22: + 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 | ^~~~~~~~ @@ -4316,32 +4383,7 @@ 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: -/usr/include/c++/14/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++/14/bits/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/info/src/info_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_impl.cc:37: -/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_impl.cc:27: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4377,12 +4419,10 @@ /usr/include/c++/14/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_group.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 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_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 | ^~~~~~~~ @@ -4396,7 +4436,7 @@ 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_composite2_op.cc:21: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4409,21 +4449,19 @@ 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_composite3_op.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_impl.cc:37: /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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3_op.cc:21: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_impl.cc:27: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4436,21 +4474,18 @@ 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/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_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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2_op.cc:21: + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4463,7 +4498,7 @@ 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_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 | ^~~~~~~~ @@ -4477,7 +4512,7 @@ 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_composite3_op.cc:21: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4487,23 +4522,24 @@ /usr/include/c++/14/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_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_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/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_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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - 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++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_quat.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4515,10 +4551,6 @@ | ^~~~~~~~ [ 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 -[ 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 -[ 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 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, @@ -4545,6 +4577,10 @@ /usr/include/c++/14/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 +[ 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 [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o @@ -4636,14 +4672,14 @@ make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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/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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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 [ 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_logger.cc.o +[ 6%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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/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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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 [ 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 @@ -4658,42 +4694,43 @@ 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=" 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' 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[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/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o -[ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o -[ 7%] 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 +[ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o +[ 7%] 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_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 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/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 -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 -[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/circle_mask.cc.o [ 7%] 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/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/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 [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o +[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/circle_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 -[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.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/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/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/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 +[ 7%] 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/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/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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.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/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4725,8 +4762,28 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 7%] 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 +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: +/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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/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++/14/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++/14/bits/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, @@ -4754,10 +4811,8 @@ 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/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/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 | ^~~~~~~~ @@ -4766,8 +4821,8 @@ from /usr/include/c++/14/cmath:3898, 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/chain_base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_base.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4777,8 +4832,6 @@ /usr/include/c++/14/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/data.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 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, @@ -4805,18 +4858,14 @@ 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/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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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 /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.hh:22: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4826,19 +4875,31 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 7%] 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/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 +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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 7%] 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 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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/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++/14/algorithm:60, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_view.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4848,26 +4909,34 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 7%] 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 +[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_algorithm.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 +[ 7%] 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 +[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.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 +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data.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 +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_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/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 +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_iterator.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_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 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/data_observer.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data_observer.cc: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: /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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data_observer.cc:26: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4877,31 +4946,28 @@ /usr/include/c++/14/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/extent_iterator.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_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/img/base/src/CMakeFiles/ost_img.dir/extent_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/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 -[ 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/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 +[ 8%] 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 [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent.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.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 -[ 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/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 -[ 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/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 -[ 8%] 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 +[ 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/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/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/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 | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4938,16 +5004,19 @@ 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/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_iterator.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent_iterator.cc:27: + 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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:30: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4962,17 +5031,21 @@ 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/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/data_observer.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data_observer.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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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: + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data_observer.cc:26: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4982,34 +5055,22 @@ /usr/include/c++/14/bits/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/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/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/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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent.cc:28: + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5019,25 +5080,19 @@ /usr/include/c++/14/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/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/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 -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_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/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 -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_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/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 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/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_iterator.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent_iterator.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_view.cc:19: + from /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:30: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5047,22 +5102,28 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/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 +[ 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/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 +[ 10%] 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 +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_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/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 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/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5072,24 +5133,24 @@ /usr/include/c++/14/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/image_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/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 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/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: /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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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: + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent.cc:28: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5099,15 +5160,19 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/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 -[ 8%] 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 +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++/14/bits/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/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/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 | ^~~~~~~~ @@ -5116,37 +5181,8 @@ from /usr/include/c++/14/cmath:3898, 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++/14/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++/14/bits/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/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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/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: + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5156,14 +5192,23 @@ /usr/include/c++/14/bits/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/editor_base.cc:22: +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++/14/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_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/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 +[ 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/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/inverted_mask.cc.o -MF CMakeFiles/ost_img.dir/inverted_mask.cc.o.d -o CMakeFiles/ost_img.dir/inverted_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/inverted_mask.cc +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_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/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 +[ 10%] 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 +[ 10%] 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/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 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, @@ -5192,11 +5237,8 @@ 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/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/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 | ^~~~~~~~ @@ -5205,9 +5247,9 @@ from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/istream:40, - from /usr/include/c++/14/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_list.cc:24: + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5217,8 +5259,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_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 +[ 10%] 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, @@ -5244,23 +5286,33 @@ /usr/include/c++/14/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/inverted_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/inverted_mask.cc.o -MF CMakeFiles/ost_img.dir/inverted_mask.cc.o.d -o CMakeFiles/ost_img.dir/inverted_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/inverted_mask.cc +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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_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 +[ 10%] 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 +[ 10%] 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/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: + 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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - 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: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5270,33 +5322,27 @@ /usr/include/c++/14/bits/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: -/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_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 -[ 10%] 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/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 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/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: /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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/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: +In file included from /usr/include/c++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5306,31 +5352,25 @@ /usr/include/c++/14/bits/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_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 -[ 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/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 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: + 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 | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/istream:40, + from /usr/include/c++/14/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_list.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5340,10 +5380,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_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 -[ 10%] 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 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, @@ -5370,8 +5406,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/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 +[ 10%] 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 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, @@ -5396,32 +5432,16 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_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 +[ 10%] 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 +[ 10%] 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 +[ 10%] 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 [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.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_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/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 -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/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 - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: -/usr/include/c++/14/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++/14/bits/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, @@ -5444,10 +5464,6 @@ /usr/include/c++/14/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/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 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] @@ -5456,8 +5472,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o -cd /build/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 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, @@ -5481,30 +5495,12 @@ /usr/include/c++/14/bits/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/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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++/14/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++/14/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/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 +[ 11%] 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 +[ 11%] 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 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] @@ -5513,25 +5509,21 @@ /usr/include/c++/14/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_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/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/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 | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5541,26 +5533,20 @@ /usr/include/c++/14/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/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 -[ 11%] 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 -[ 11%] 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 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/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 | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5570,32 +5556,18 @@ /usr/include/c++/14/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/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 -[ 11%] 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 -[ 11%] 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 -[ 12%] 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/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/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: /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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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 /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5605,28 +5577,27 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 12%] 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 -[ 12%] 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 +[ 12%] 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 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: + 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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/istream:40, - from /usr/include/c++/14/fstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/peak.cc:25: +In file included from /usr/include/c++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5636,22 +5607,32 @@ /usr/include/c++/14/bits/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++/14/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/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 -[ 12%] 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 +[ 12%] 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 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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query.cc:23: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5661,24 +5642,23 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 12%] 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 -[ 12%] 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 +[ 12%] 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/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/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: /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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/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: + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5691,17 +5671,17 @@ 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/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/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5711,6 +5691,12 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 12%] 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 +[ 12%] 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 +[ 12%] 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 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, @@ -5743,20 +5729,40 @@ /usr/include/c++/14/bits/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{ - | ^~~~~~~~ +[ 12%] 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/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: +/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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/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++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 12%] 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/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/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: /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 | ^~~~~~~~ @@ -5765,7 +5771,7 @@ from /usr/include/c++/14/cmath:3898, 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/img/image.hh:32: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5775,10 +5781,6 @@ /usr/include/c++/14/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/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 -[ 12%] 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, @@ -5807,16 +5809,14 @@ 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/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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:30: + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_view.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5826,24 +5826,26 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 13%] 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 -[ 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 +[ 12%] 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 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/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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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: + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/istream:40, + from /usr/include/c++/14/fstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/peak.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5856,14 +5858,20 @@ 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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_view.cc:19: + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5873,28 +5881,32 @@ /usr/include/c++/14/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/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/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 -[ 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 -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o +[ 12%] 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/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 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/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 +[ 12%] 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 +[ 12%] 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/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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:22: +In file included from /usr/include/c++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5907,15 +5919,18 @@ 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/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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.cc:25: + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5925,20 +5940,21 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 12%] 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/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/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:30: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5948,19 +5964,33 @@ /usr/include/c++/14/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/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 +[ 12%] 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 +[ 12%] 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%] 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 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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/view_op.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5970,50 +6000,30 @@ /usr/include/c++/14/bits/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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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++/14/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/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 13%] 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 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/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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/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: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6023,14 +6033,6 @@ /usr/include/c++/14/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/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -[ 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_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 -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/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, @@ -6060,19 +6062,20 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 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/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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/deque:62, - from /usr/include/c++/14/stack:62, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_info_convert.cc:25: + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6082,14 +6085,6 @@ /usr/include/c++/14/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/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/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 -[ 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 [ 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 [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o @@ -6099,37 +6094,10 @@ 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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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++/14/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++/14/bits/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/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/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 | ^~~~~~~~ @@ -6140,8 +6108,7 @@ 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/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: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6151,73 +6118,33 @@ /usr/include/c++/14/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/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/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 | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/view_op.cc:24: -/usr/include/c++/14/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++/14/bits/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++/14/bits/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: + 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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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++/14/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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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++/14/bits/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/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 - | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, @@ -6232,22 +6159,30 @@ /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 | ^~~~~~~~ +/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /usr/include/c++/14/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 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/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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - 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/img/vecmat.hh:30: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6257,24 +6192,22 @@ /usr/include/c++/14/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/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/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/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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/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/coord_source.hh:25: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6292,20 +6225,24 @@ /usr/include/c++/14/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/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/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/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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.cc:19: + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6340,16 +6277,10 @@ /usr/include/c++/14/bits/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{ - | ^~~~~~~~ -/usr/include/c++/14/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 +[ 15%] 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 +[ 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 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] @@ -6358,26 +6289,18 @@ /usr/include/c++/14/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/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/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/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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - 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: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6387,33 +6310,16 @@ /usr/include/c++/14/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/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/modules/mol/base/src/impl/connector_impl.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.cc:19: -/usr/include/c++/14/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/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{ + | ^~~~~~~~ /usr/include/c++/14/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_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, @@ -6440,25 +6346,18 @@ /usr/include/c++/14/bits/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: -/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++/14/bits/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/entity_impl.cc:35: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/stl_tree.h:63, - from /usr/include/c++/14/map:62, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.cc:22: + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6468,6 +6367,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 15%] 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 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] @@ -6477,15 +6378,15 @@ 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: + 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++/14/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 +[ 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, @@ -6509,8 +6410,125 @@ /usr/include/c++/14/bits/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/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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/stl_tree.h:63, + from /usr/include/c++/14/map:62, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.cc:22: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 15%] 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/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 15%] 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 +[ 15%] 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 +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: +/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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/deque:62, + from /usr/include/c++/14/stack:62, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_info_convert.cc:25: +/usr/include/c++/14/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++/14/bits/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/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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/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++/14/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 [ 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 +[ 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 +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: +/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++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/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: +/usr/include/c++/14/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++/14/bits/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, @@ -6535,28 +6553,19 @@ /usr/include/c++/14/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 -[ 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 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/impl/residue_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/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/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/residue_impl.cc:19: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/raster_image/raster_image.cc:31: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6566,34 +6575,6 @@ /usr/include/c++/14/bits/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++/14/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 -[ 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/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/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/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 -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 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, @@ -6644,6 +6625,41 @@ /usr/include/c++/14/bits/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_handle.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/residue_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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/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/residue_impl.cc:19: +/usr/include/c++/14/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++/14/bits/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++/14/bits/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] @@ -6652,6 +6668,57 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 16%] Linking CXX shared module ../../../stage/lib/python3.12/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/python3.12/dist-packages/ost/_ost_base.so CMakeFiles/_ost_base.dir/wrap_base.cc.o CMakeFiles/_ost_base.dir/export_logger.cc.o CMakeFiles/_ost_base.dir/export_range.cc.o CMakeFiles/_ost_base.dir/export_units.cc.o -L/build/reproducible-path/openstructure-2.5.0/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/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.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/python3.12/dist-packages//ost/./settings.pyc\",\"settings.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/stutil.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./stutil.pyc\",\"stutil.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.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/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/python3.12/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/python3.12/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/python3.12/dist-packages//ost/./testutils.pyc\",\"testutils.py\",doraise=True)" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 16%] 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' +[ 16%] 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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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 +[ 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 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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/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 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/usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/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 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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/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 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, @@ -6659,16 +6726,17 @@ 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.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/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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/anisotropic.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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6678,20 +6746,15 @@ /usr/include/c++/14/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/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 -[ 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 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/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/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: /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 | ^~~~~~~~ @@ -6699,7 +6762,8 @@ from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6717,8 +6781,8 @@ 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/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/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 | ^~~~~~~~ @@ -6736,26 +6800,23 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 17%] Linking CXX shared module ../../../stage/lib/python3.12/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 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/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/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: /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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/anisotropic.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6765,27 +6826,16 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/_ost_base.so CMakeFiles/_ost_base.dir/wrap_base.cc.o CMakeFiles/_ost_base.dir/export_logger.cc.o CMakeFiles/_ost_base.dir/export_range.cc.o CMakeFiles/_ost_base.dir/export_units.cc.o -L/build/reproducible-path/openstructure-2.5.0/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/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.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 -[ 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 -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/python3.12/dist-packages//ost/./settings.pyc\",\"settings.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/stutil.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./stutil.pyc\",\"stutil.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.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.12/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/python3.12/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/python3.12/dist-packages//ost/./xmlrunner.pyc\",\"xmlrunner.py\",doraise=True)" -[ 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 -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/python3.12/dist-packages//ost/./testutils.pyc\",\"testutils.py\",doraise=True)" -make[3]: Leaving 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/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/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/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: /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 | ^~~~~~~~ @@ -6793,8 +6843,7 @@ from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, 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/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6804,13 +6853,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 17%] 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' 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, @@ -6819,16 +6861,16 @@ 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/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/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 | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6838,19 +6880,16 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 17%] 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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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 -[ 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 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/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/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: /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 | ^~~~~~~~ @@ -6858,8 +6897,7 @@ from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, 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/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6869,18 +6907,10 @@ /usr/include/c++/14/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.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 [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_laplacian.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 -[ 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/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 -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/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 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, @@ -6909,33 +6939,8 @@ /usr/include/c++/14/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/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/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: -/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian.cc:25: -/usr/include/c++/14/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++/14/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/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/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 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, @@ -6965,19 +6970,23 @@ 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_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/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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_gradient_magnitude.cc:25: + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/info/pymod/wrap_info.cc:27: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6987,22 +6996,28 @@ /usr/include/c++/14/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/histogram.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/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/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/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: /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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7044,16 +7059,15 @@ 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/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/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_gradient_magnitude.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7094,33 +7108,22 @@ | ^~~~~~~~ [ 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 -[ 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 -[ 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 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/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/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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/local_sigma_threshold.cc:20: + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7130,28 +7133,23 @@ /usr/include/c++/14/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_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/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: + 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: /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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/info/pymod/wrap_info.cc:27: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7161,10 +7159,8 @@ /usr/include/c++/14/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 -[ 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 +[ 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 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, @@ -7173,15 +7169,19 @@ 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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/local_sigma_threshold.cc:20: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7191,10 +7191,30 @@ /usr/include/c++/14/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_factory.cc.o +[ 18%] Linking CXX shared library ../../../../stage/lib/libost_mol.so +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 +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 +[ 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 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/usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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 +[ 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 +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' +[ 18%] Built target ost_mol +[ 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 [ 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, @@ -7202,8 +7222,8 @@ 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/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/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 | ^~~~~~~~ @@ -7226,11 +7246,11 @@ 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/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 | ^~~~~~~~ @@ -7238,8 +7258,7 @@ from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, 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/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7249,30 +7268,24 @@ /usr/include/c++/14/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/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 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/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/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: /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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/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: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7282,11 +7295,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 20%] Linking CXX shared library ../../../../stage/lib/libost_mol.so -cd /build/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 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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 -[ 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, @@ -7296,8 +7304,8 @@ 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_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/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 | ^~~~~~~~ @@ -7318,8 +7326,6 @@ /usr/include/c++/14/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 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, @@ -7355,20 +7361,16 @@ 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/normalizer_impl.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_od.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_od.cc:24: + 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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/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: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7378,21 +7380,8 @@ /usr/include/c++/14/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 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' -[ 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%] Built target ost_mol -make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 20%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.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 -[ 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/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 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, @@ -7401,15 +7390,20 @@ 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/smooth_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_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 | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7419,6 +7413,8 @@ /usr/include/c++/14/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_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 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, @@ -7427,16 +7423,20 @@ 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/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/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_od.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_od.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7446,12 +7446,8 @@ /usr/include/c++/14/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/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/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 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, @@ -7477,6 +7473,20 @@ /usr/include/c++/14/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/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 +make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 20%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.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 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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/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 In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, @@ -7487,8 +7497,7 @@ 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_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/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 | ^~~~~~~~ @@ -7506,6 +7515,8 @@ /usr/include/c++/14/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/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 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, @@ -7531,26 +7542,19 @@ /usr/include/c++/14/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/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 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/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/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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - 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/transformation_base.hh:30: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7568,8 +7572,8 @@ 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/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/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 | ^~~~~~~~ @@ -7590,16 +7594,21 @@ 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/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: + 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/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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/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: + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7614,14 +7623,16 @@ 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/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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformation_base.hh:30: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7631,8 +7642,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o -cd /build/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 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, @@ -7660,13 +7669,18 @@ /usr/include/c++/14/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/rscrosscorr.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/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 +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 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/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/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: /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 | ^~~~~~~~ @@ -7674,7 +7688,7 @@ from /usr/include/c++/14/string:47, from /usr/include/c++/14/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 /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/discrete_shrink.cc:21: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7684,24 +7698,26 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/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, 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/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7711,31 +7727,21 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/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 [ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.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_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/sequence_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/aligned_region.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 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/fractional_shift.cc:26: + 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 | ^~~~~~~~ +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 In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fractional_shift.cc:25: + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7745,25 +7751,29 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_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/aligned_region.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/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_column.cc.o -MF CMakeFiles/ost_seq.dir/aligned_column.cc.o.d -o CMakeFiles/ost_seq.dir/aligned_column.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/aligned_column.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/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/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/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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7775,24 +7785,23 @@ | ^~~~~~~~ [ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.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_list.cc.o -MF CMakeFiles/ost_seq.dir/sequence_list.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_list.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_list.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/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 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_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/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 | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7802,15 +7811,17 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 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/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 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/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/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 | ^~~~~~~~ @@ -7818,7 +7829,7 @@ from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, 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/polar.hh:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7828,8 +7839,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 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 -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_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 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, @@ -7857,11 +7866,11 @@ 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/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: + 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: /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 | ^~~~~~~~ @@ -7869,8 +7878,7 @@ from /usr/include/c++/14/string:47, from /usr/include/c++/14/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: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:30: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7923,10 +7931,10 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 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 -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_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 [ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/views_from_sequences.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/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 -[ 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/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, @@ -7934,16 +7942,16 @@ 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_column.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/aligned_column.cc:19: + 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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7953,29 +7961,25 @@ /usr/include/c++/14/bits/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 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/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/sequence_list.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/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/base/src/aligned_column.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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7985,11 +7989,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 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 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: + 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{ | ^~~~~~~~ @@ -8038,28 +8039,21 @@ /usr/include/c++/14/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/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 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/base/src/sequence_op.cc:23: + 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: /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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/istream:40, - from /usr/include/c++/14/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_op.cc:19: + from /usr/include/c++/14/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: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8069,6 +8063,20 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 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 +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] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/14/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/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 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, @@ -8105,6 +8113,34 @@ /usr/include/c++/14/bits/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/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_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 + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/istream:40, + from /usr/include/c++/14/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_op.cc:19: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ [ 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 @@ -8121,38 +8157,38 @@ 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[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 -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]: 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 -[ 22%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -[ 22%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -[ 22%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o -[ 22%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o 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/c++ -DBOOST_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 -[ 22%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/ins_del.cc.o -[ 22%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/distance_map.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 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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/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/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_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/contact_weight_matrix.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/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 -[ 22%] 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/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 +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]: 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 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/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/ins_del.cc.o -MF CMakeFiles/ost_seq_alg.dir/ins_del.cc.o.d -o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/ins_del.cc -[ 22%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/entropy.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/local_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/local_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/local_align.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/local_align.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/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 [ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.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/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/db/src/CMakeFiles/ost_db.dir/linear_indexer.cc.o +[ 24%] 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/usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/binary_container.cc.o -MF CMakeFiles/ost_db.dir/binary_container.cc.o.d -o CMakeFiles/ost_db.dir/binary_container.cc.o -c /build/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 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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/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/contact_weight_matrix.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 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CMakeFiles/ost_seq_alg.dir/distance_map.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/distance_map.cc +[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/entropy.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/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 +[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/global_align.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/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 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)': @@ -8162,6 +8198,8 @@ /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; | ^ +[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/ins_del.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/ins_del.cc.o -MF CMakeFiles/ost_seq_alg.dir/ins_del.cc.o.d -o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/ins_del.cc 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] @@ -8220,6 +8258,31 @@ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:2372:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2372 | for (i=1;i struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/clip_alignment.cc:24: +/usr/include/c++/14/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++/14/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 TMalign_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:3289:12: warning: variable 'Lnorm_d0' set but not used [-Wunused-but-set-variable] 3289 | double Lnorm_d0; @@ -8241,14 +8304,20 @@ /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 struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/14/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/se.h:222:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 222 | for (int r=0;r >::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 struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -8292,30 +8373,10 @@ /usr/include/c++/14/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 > >&, 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 struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h: In function 'int TMalign_dimer_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, bool**, std::vector >, 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; | ^~~~~~~~ -/usr/include/c++/14/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 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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 3016 | for (i=0;i struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/14/bits/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, @@ -8336,14 +8405,15 @@ 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/seq/alg/clip_alignment.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/clip_alignment.cc:25: + 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/conservation.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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/clip_alignment.cc:24: + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8368,15 +8438,16 @@ 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: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/db/src/extract_data_helper.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.hh:22: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8386,21 +8457,6 @@ /usr/include/c++/14/bits/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++/14/bits/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/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: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.hh:22: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8465,109 +8516,16 @@ /usr/include/c++/14/bits/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++/14/bits/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/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/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++/14/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++/14/bits/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++/14/bits/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_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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/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++/14/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++/14/bits/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_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: -/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/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++/14/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/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{ | ^~~~~~~~ @@ -8575,19 +8533,17 @@ 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/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++/14/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] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/14/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/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/merge_pairwise_alignments.cc.o -MF CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o.d -o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/merge_pairwise_alignments.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] @@ -8632,8 +8590,6 @@ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:263:44: note: the temporary was destroyed at the end of the full expression 'ost::seq::SequenceList::operator[](int) const(i).ost::seq::SequenceHandle::GetString()' 263 | const std::string& s = seq[i].GetString(); | ~~~~~~~~~~~~~~~~^~ -[ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/pair_subst_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 -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 In file included from /usr/include/c++/14/string:54, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, @@ -8729,16 +8685,15 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ +[ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/pair_subst_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 -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/semiglobal_align.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/semiglobal_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/semiglobal_align.cc [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o cd /build/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_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 -[ 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 CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/subst_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 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/subst_weight_matrix.cc -[ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/variance_map.cc.o -cd /build/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/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 +[ 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, @@ -8747,8 +8702,8 @@ 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/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 | ^~~~~~~~ @@ -8757,9 +8712,36 @@ from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/istream:40, - from /usr/include/c++/14/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/merge_pairwise_alignments.cc:21: + from /usr/include/c++/14/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++/14/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++/14/bits/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_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: +/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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8777,10 +8759,39 @@ /usr/include/c++/14/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 -[ 25%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/binary_container.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/binary_container.cc.o -MF CMakeFiles/ost_db.dir/binary_container.cc.o.d -o CMakeFiles/ost_db.dir/binary_container.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/src/binary_container.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++/14/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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++/14/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++/14/bits/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/db/extract_data_helper.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/db/src/extract_data_helper.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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9039,61 +9005,41 @@ /usr/include/c++/14/bits/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{ - | ^~~~~~~~ +/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/istream:40, + from /usr/include/c++/14/fstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/variance_map.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9235,22 +9191,34 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/rule_based.cc.o +cd /build/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 +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++/14/bits/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/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/xcs_editor.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/heuristic.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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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: + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9260,21 +9228,28 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/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/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 +[ 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/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 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/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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/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: + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9284,14 +9259,24 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/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) + | ^~~~~~~~~ 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/modules/conop/src/model_check.hh:4, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/model_check.cc:1: + 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: /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 | ^~~~~~~~ @@ -9299,8 +9284,8 @@ from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, 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: + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9310,77 +9295,80 @@ /usr/include/c++/14/bits/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] + 32 | : public std::iterator{ + | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/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/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 [ 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_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 -[ 26%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/info/_ost_info.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_info.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/info/_ost_info.so CMakeFiles/_ost_info.dir/wrap_info.cc.o -L/build/reproducible-path/openstructure-2.5.0/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 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 ../../../stage/lib/libost_base.so.2.5.0 ../../../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 [ 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/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 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/info/./__init__.pyc\",\"__init__.py\",doraise=True)" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 26%] Built target _ost_info make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/depend -make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/depend make[3]: Entering directory '/build/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/c++ -DBOOST_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 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/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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/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++/14/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++/14/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' +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' +[ 26%] 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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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' 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' -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' [ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o -[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o -[ 26%] 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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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 +[ 26%] 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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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 +[ 26%] 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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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 -[ 26%] 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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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 -[ 26%] Linking CXX shared library ../../../../stage/lib/libost_seq_alg.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_alg.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_seq_alg.so.2.5 -o ../../../../stage/lib/libost_seq_alg.so.2.5.0 CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o CMakeFiles/ost_seq_alg.dir/conservation.cc.o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/distance_map.cc.o CMakeFiles/ost_seq_alg.dir/entropy.cc.o CMakeFiles/ost_seq_alg.dir/global_align.cc.o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o CMakeFiles/ost_seq_alg.dir/local_align.cc.o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/variance_map.cc.o CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -L/build/reproducible-path/openstructure-2.5.0/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 /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 -[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom_view.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_atom_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_atom_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_atom_view.cc -[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o -MF CMakeFiles/_ost_mol.dir/export_bond.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bond.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bond.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_seq_alg.so.2.5 ../../../../stage/lib/libost_seq_alg.so -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 26%] Built target ost_seq_alg -[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain.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/compound_lib_base.hh:5, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib.cc:28: + 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 | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib.cc:24: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9390,6 +9378,15 @@ /usr/include/c++/14/bits/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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib.cc:24: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, @@ -9508,79 +9534,10 @@ | ^~~~ [ 26%] 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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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 -/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 >, int)': -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:545:21: warning: 'invmap' may be used uninitialized [-Wmaybe-uninitialized] - 545 | NWalign_main(seqx, seqy, xlen, ylen, sequence[0],sequence[1], - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 546 | mol_type, invmap, 0, glocal); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:535:14: note: 'invmap' was declared here - 535 | int *invmap; - | ^~~~~~ -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/base/pymod/export_data_algorithm.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_data_algorithm.cc:25: -/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_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/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/pymod/wrap_extent_iterator.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_extent.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_extent.cc:25: -/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o -MF CMakeFiles/_ost_mol.dir/export_bond.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bond.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bond.cc +[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain.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, @@ -9612,6 +9569,9 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 26%] Linking CXX shared library ../../../../stage/lib/libost_seq_alg.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_alg.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_seq_alg.so.2.5 -o ../../../../stage/lib/libost_seq_alg.so.2.5.0 CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o CMakeFiles/ost_seq_alg.dir/conservation.cc.o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/distance_map.cc.o CMakeFiles/ost_seq_alg.dir/entropy.cc.o CMakeFiles/ost_seq_alg.dir/global_align.cc.o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o CMakeFiles/ost_seq_alg.dir/local_align.cc.o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/variance_map.cc.o CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -L/build/reproducible-path/openstructure-2.5.0/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 /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, @@ -9645,11 +9605,11 @@ 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/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/pymod/export_chain.cc:23: + 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/base/pymod/export_data_algorithm.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 | ^~~~~~~~ @@ -9663,7 +9623,7 @@ 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/mol/base/pymod/export_chain.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_data_algorithm.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9673,14 +9633,24 @@ /usr/include/c++/14/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 >, int)': +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:545:21: warning: 'invmap' may be used uninitialized [-Wmaybe-uninitialized] + 545 | NWalign_main(seqx, seqy, xlen, ylen, sequence[0],sequence[1], + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 546 | mol_type, invmap, 0, glocal); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:535:14: note: 'invmap' was declared here + 535 | int *invmap; + | ^~~~~~ +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_seq_alg.so.2.5 ../../../../stage/lib/libost_seq_alg.so 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/pymod/export_atom_view.cc:24: + 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/pymod/wrap_extent_iterator.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_extent.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 | ^~~~~~~~ @@ -9694,7 +9664,7 @@ 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/mol/base/pymod/export_atom_view.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_extent.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9704,6 +9674,10 @@ /usr/include/c++/14/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' +[ 26%] Built target ost_seq_alg +[ 26%] 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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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 /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, @@ -9711,7 +9685,7 @@ 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/pymod/export_bond.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_atom_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 | ^~~~~~~~ @@ -9725,7 +9699,7 @@ 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/mol/base/pymod/export_bond.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_atom_view.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9735,8 +9709,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_group.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_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, @@ -9768,8 +9740,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 26%] 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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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 [ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o -MF CMakeFiles/_ost_img.dir/export_phase.cc.o.d -o CMakeFiles/_ost_img.dir/export_phase.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_phase.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, @@ -9779,7 +9749,7 @@ 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/pymod/export_chain_view.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain.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 | ^~~~~~~~ @@ -9793,7 +9763,7 @@ 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/mol/base/pymod/export_chain_view.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9803,15 +9773,14 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o -MF CMakeFiles/_ost_img.dir/export_point.cc.o.d -o CMakeFiles/_ost_img.dir/export_point.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_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/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/coord_group.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_coord_group.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/pymod/export_bond.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 | ^~~~~~~~ @@ -9825,7 +9794,7 @@ 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/mol/base/pymod/export_coord_group.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bond.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9835,6 +9804,10 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o -MF CMakeFiles/_ost_img.dir/export_point.cc.o.d -o CMakeFiles/_ost_img.dir/export_point.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_point.cc +[ 27%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_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, @@ -9865,8 +9838,31 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 27%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_coord_frame.cc +[ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o -MF CMakeFiles/_ost_img.dir/export_progress.cc.o.d -o CMakeFiles/_ost_img.dir/export_progress.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_progress.cc +In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/string:43, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/istream:40, + from /usr/include/c++/14/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/basic_fun.h:12, + from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/param_set.h:7: +In member function 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]', + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]' at /usr/include/c++/14/bits/alloc_traits.h:534:17, + inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/vector.tcc:634:26, + inlined from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/vector.tcc:123:21, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:1301:21, + inlined from 'int trimComplex(std::vector > >&, std::vector >&, std::vector >&, std::vector&, const std::vector > >&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, int, int)' at /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:2941:33: +/usr/include/c++/14/bits/new_allocator.h:191:11: warning: 'dinter' may be used uninitialized [-Wmaybe-uninitialized] + 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h: In function 'int trimComplex(std::vector > >&, std::vector >&, std::vector >&, std::vector&, const std::vector > >&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, int, int)': +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:2894:12: note: 'dinter' was declared here + 2894 | double dinter; + | ^~~~~~ 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, @@ -9897,52 +9893,17 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o -MF CMakeFiles/_ost_img.dir/export_progress.cc.o.d -o CMakeFiles/_ost_img.dir/export_progress.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_progress.cc -In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/string:43, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/istream:40, - from /usr/include/c++/14/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/basic_fun.h:12, - from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/param_set.h:7: -In member function 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]', - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair; _Args = {std::pair}; _Tp = std::pair]' at /usr/include/c++/14/bits/alloc_traits.h:534:17, - inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/vector.tcc:634:26, - inlined from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/vector.tcc:123:21, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:1301:21, - inlined from 'int trimComplex(std::vector > >&, std::vector >&, std::vector >&, std::vector&, const std::vector > >&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, int, int)' at /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:2941:33: -/usr/include/c++/14/bits/new_allocator.h:191:11: warning: 'dinter' may be used uninitialized [-Wmaybe-uninitialized] - 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h: In function 'int trimComplex(std::vector > >&, std::vector >&, std::vector >&, std::vector&, const std::vector > >&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, int, int)': -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:2894:12: note: 'dinter' was declared here - 2894 | double dinter; - | ^~~~~~ [ 27%] Linking CXX shared library ../../../stage/lib/libost_conop.so cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_conop.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_conop.so.2.5 -o ../../../stage/lib/libost_conop.so.2.5.0 CMakeFiles/ost_conop.dir/processor.cc.o CMakeFiles/ost_conop.dir/amino_acids.cc.o CMakeFiles/ost_conop.dir/conop.cc.o CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o CMakeFiles/ost_conop.dir/compound_lib_base.cc.o CMakeFiles/ost_conop.dir/heuristic.cc.o CMakeFiles/ost_conop.dir/diag.cc.o CMakeFiles/ost_conop.dir/rule_based.cc.o CMakeFiles/ost_conop.dir/model_check.cc.o CMakeFiles/ost_conop.dir/compound.cc.o CMakeFiles/ost_conop.dir/compound_lib.cc.o CMakeFiles/ost_conop.dir/ring_finder.cc.o -L/build/reproducible-path/openstructure-2.5.0/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_db.so.2.5.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../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 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_conop.so.2.5 ../../../stage/lib/libost_conop.so -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 27%] Built target ost_conop -make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/depend -make[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.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 27%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.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/svd_superpose.cc.o -MF CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o.d -o CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/svd_superpose.cc -[ 27%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o -MF CMakeFiles/_ost_mol.dir/export_editors.cc.o.d -o CMakeFiles/_ost_mol.dir/export_editors.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_editors.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/modules/mol/base/pymod/export_coord_frame.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/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/pymod/export_chain_view.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 | ^~~~~~~~ @@ -9956,7 +9917,7 @@ 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/mol/base/pymod/export_coord_frame.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain_view.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9966,6 +9927,13 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o -MF CMakeFiles/_ost_img.dir/export_raster_image.cc.o.d -o CMakeFiles/_ost_img.dir/export_raster_image.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_raster_image.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_conop.so.2.5 ../../../stage/lib/libost_conop.so +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 27%] Built target ost_conop +[ 27%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_group.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_coord_group.cc /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc: In function 'ost::bindings::MMAlignResult ost::bindings::WrappedMMAlign(const std::vector&, const std::vector&, const ost::seq::SequenceList&, const ost::seq::SequenceList&, const std::vector&, const std::vector&, bool)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:896:36: warning: 'seqx' may be used uninitialized [-Wmaybe-uninitialized] 896 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, @@ -10023,8 +9991,26 @@ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:549:18: note: 'secy' was declared here 549 | char *secx, *secy; // for the secondary structure | ^~~~ -[ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o -MF CMakeFiles/_ost_img.dir/export_raster_image.cc.o.d -o CMakeFiles/_ost_img.dir/export_raster_image.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_raster_image.cc +[ 27%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_coord_frame.cc +make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/depend +make[3]: Entering directory '/build/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.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 27%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.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/svd_superpose.cc.o -MF CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o.d -o CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/svd_superpose.cc +make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/depend +make[3]: Entering directory '/build/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.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 27%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.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/bitmap_io.cc.o -MF CMakeFiles/ost_gfx.dir/bitmap_io.cc.o.d -o CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/bitmap_io.cc +[ 27%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.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/clash_score.cc.o -MF CMakeFiles/ost_mol_alg.dir/clash_score.cc.o.d -o CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/clash_score.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, @@ -10046,74 +10032,12 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o -MF CMakeFiles/_ost_img.dir/export_size.cc.o.d -o CMakeFiles/_ost_img.dir/export_size.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_size.cc -[ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o -MF CMakeFiles/_ost_img.dir/export_mask.cc.o.d -o CMakeFiles/_ost_img.dir/export_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_mask.cc -[ 27%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity.cc -[ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity_view.cc -[ 30%] Linking CXX shared library ../../../stage/lib/libost_bindings.so +[ 29%] 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/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/pymod/export_editors.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_editors.cc:19: -/usr/include/c++/14/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++/14/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/bindings/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_bindings.so.2.5.0 ../../../stage/lib/libost_bindings.so.2.5 ../../../stage/lib/libost_bindings.so -[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o -MF CMakeFiles/_ost_mol.dir/export_property_id.cc.o.d -o CMakeFiles/_ost_mol.dir/export_property_id.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_property_id.cc -make[3]: Leaving 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/mol/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_editors.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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 30%] Built target ost_bindings -make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.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/bitmap_io.cc.o -MF CMakeFiles/ost_gfx.dir/bitmap_io.cc.o.d -o CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/bitmap_io.cc -[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o -MF CMakeFiles/_ost_mol.dir/export_query.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_query.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/raster_image/raster_image.hh:31, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_raster_image.cc:28: @@ -10140,58 +10064,31 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_residue.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/modules/img/base/pymod/export_size.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_size.cc:25: -/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 29%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.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/exporter.cc.o -MF CMakeFiles/ost_gfx.dir/exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/exporter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/exporter.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_bindings.so.2.5.0 ../../../stage/lib/libost_bindings.so.2.5 ../../../stage/lib/libost_bindings.so +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 29%] Built target ost_bindings +[ 29%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/collada_exporter.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/collada_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/collada_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/collada_exporter.cc +[ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o -MF CMakeFiles/_ost_img.dir/export_size.cc.o.d -o CMakeFiles/_ost_img.dir/export_size.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_size.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/polygon_mask.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/mask.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_mask.cc: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/clash_score.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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_mask.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/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10201,17 +10098,11 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o -cd /build/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/exporter.cc.o -MF CMakeFiles/ost_gfx.dir/exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/exporter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/exporter.cc -[ 30%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o -MF CMakeFiles/_ost_img.dir/export_image_list.cc.o.d -o CMakeFiles/_ost_img.dir/export_image_list.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_image_list.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/modules/mol/base/pymod/export_entity.cc:23: + 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/modules/mol/base/pymod/export_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 | ^~~~~~~~ @@ -10225,7 +10116,7 @@ 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/mol/base/pymod/export_entity.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_coord_frame.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10235,21 +10126,13 @@ /usr/include/c++/14/bits/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/pymod/export_entity.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++/14/bits/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/modules/mol/base/pymod/export_entity_view.cc:29: + 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/coord_group.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_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 | ^~~~~~~~ @@ -10263,7 +10146,7 @@ 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/mol/base/pymod/export_entity_view.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_coord_group.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10273,30 +10156,29 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 30%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o -MF CMakeFiles/_ost_img.dir/export_map.cc.o.d -o CMakeFiles/_ost_img.dir/export_map.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_map.cc +[ 29%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.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_structure_segments.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_structure_segments.cc +[ 29%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.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/local_dist_diff_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.cc +[ 29%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color.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.cc.o -MF CMakeFiles/ost_gfx.dir/color.cc.o.d -o CMakeFiles/ost_gfx.dir/color.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.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/pymod/export_property_id.cc:24: + 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/collada_exporter.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_property_id.cc:19: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/istream:40, + from /usr/include/c++/14/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/collada_exporter.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10333,58 +10215,18 @@ 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/pymod/export_query.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_query.cc:19: -/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 30%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.cc.o -MF CMakeFiles/_ost_img.dir/wrap_img.cc.o.d -o CMakeFiles/_ost_img.dir/wrap_img.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/wrap_img.cc -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/collada_exporter.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/collada_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/collada_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/collada_exporter.cc -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color.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.cc.o -MF CMakeFiles/ost_gfx.dir/color.cc.o.d -o CMakeFiles/ost_gfx.dir/color.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.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/pymod/export_residue.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_structure_segments.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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_residue.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/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10394,6 +10236,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 29%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/primitives.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/primitives.cc.o -MF CMakeFiles/ost_gfx.dir/primitives.cc.o.d -o CMakeFiles/ost_gfx.dir/primitives.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/primitives.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, @@ -10421,75 +10265,11 @@ 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/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/base/pymod/export_image_list.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_image_list.cc:25: -/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_residue_view.cc -[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o -MF CMakeFiles/_ost_mol.dir/export_surface.cc.o.d -o CMakeFiles/_ost_mol.dir/export_surface.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_surface.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/image.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_map.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_map.cc:20: -/usr/include/c++/14/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++/14/bits/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/collada_exporter.cc: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/local_dist_diff_test.cc:4: /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 | ^~~~~~~~ @@ -10497,10 +10277,8 @@ from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/istream:40, - from /usr/include/c++/14/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/collada_exporter.cc:24: + from /usr/include/c++/14/iomanip:42, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.cc:1: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10510,18 +10288,30 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -MF CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bounding_box.cc -[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_query_view_wrapper.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/local_dist_diff_test.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.cc:6: +/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 29%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_test_common.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/distance_test_common.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_test_common.cc +[ 29%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.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/entity.cc.o -MF CMakeFiles/ost_gfx.dir/entity.cc.o.d -o CMakeFiles/ost_gfx.dir/entity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/entity.cc +[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.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/symmetry_node.cc.o -MF CMakeFiles/ost_gfx.dir/symmetry_node.cc.o.d -o CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/symmetry_node.cc +[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.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/gfx_node.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_node.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_node.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_node.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/base/pymod/wrap_img.cc:33: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_size.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 | ^~~~~~~~ @@ -10535,7 +10325,7 @@ 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/img/base/pymod/wrap_img.cc:27: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_size.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10545,34 +10335,24 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o -MF CMakeFiles/_ost_mol.dir/export_torsion.cc.o.d -o CMakeFiles/_ost_mol.dir/export_torsion.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_torsion.cc -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/primitives.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/primitives.cc.o -MF CMakeFiles/ost_gfx.dir/primitives.cc.o.d -o CMakeFiles/ost_gfx.dir/primitives.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/primitives.cc -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.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/entity.cc.o -MF CMakeFiles/ost_gfx.dir/entity.cc.o.d -o CMakeFiles/ost_gfx.dir/entity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/entity.cc +[ 30%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o -MF CMakeFiles/_ost_img.dir/export_mask.cc.o.d -o CMakeFiles/_ost_img.dir/export_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_mask.cc +[ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.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/distance_rmsd_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.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/pymod/export_residue_view.cc:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/primitives.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/primitives.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_residue_view.cc:19: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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/gl_helper.hh:36, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/primitives.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10582,11 +10362,15 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 30%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o -MF CMakeFiles/_ost_img.dir/export_image_list.cc.o.d -o CMakeFiles/_ost_img.dir/export_image_list.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_image_list.cc +[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o -MF CMakeFiles/_ost_mol.dir/export_editors.cc.o.d -o CMakeFiles/_ost_mol.dir/export_editors.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_editors.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/primitives.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/primitives.cc:27: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/symmetry_node.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/symmetry_node.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 | ^~~~~~~~ @@ -10595,7 +10379,7 @@ from /usr/include/c++/14/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/gl_helper.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/primitives.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/symmetry_node.cc:20: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10608,23 +10392,20 @@ 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/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/pymod/export_surface.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_view.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/distance_test_common.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_test_common.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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_surface.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/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10634,8 +10415,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.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/symmetry_node.cc.o -MF CMakeFiles/ost_gfx.dir/symmetry_node.cc.o.d -o CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/symmetry_node.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, @@ -10658,6 +10437,10 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o +[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.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/gfx_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_object.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.cc +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/superpose_frames.cc.o -MF CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o.d -o CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/superpose_frames.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/impl/trace_renderer_base.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh:31, @@ -10674,75 +10457,20 @@ 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/base/pymod/export_bounding_box.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bounding_box.cc:19: -/usr/include/c++/14/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++/14/bits/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/modules/mol/base/pymod/export_query_view_wrapper.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_query_view_wrapper.cc:19: -/usr/include/c++/14/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++/14/bits/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/symmetry_node.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/symmetry_node.cc:21: + 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/distance_rmsd_test.cc:2: /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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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/gl_helper.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/symmetry_node.cc:20: + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/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/distance_rmsd_test.cc:1: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10752,53 +10480,17 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 31%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.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/clash_score.cc.o -MF CMakeFiles/ost_mol_alg.dir/clash_score.cc.o.d -o CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/clash_score.cc -[ 31%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o -MF CMakeFiles/_ost_mol.dir/export_visitor.cc.o.d -o CMakeFiles/_ost_mol.dir/export_visitor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_visitor.cc -[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.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/gfx_node.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_node.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_node.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_node.cc -[ 31%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/img/_ost_img.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/img/_ost_img.so CMakeFiles/_ost_img.dir/export_data.cc.o CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o CMakeFiles/_ost_img.dir/export_extent.cc.o CMakeFiles/_ost_img.dir/export_image_handle.cc.o CMakeFiles/_ost_img.dir/export_peak.cc.o CMakeFiles/_ost_img.dir/export_phase.cc.o CMakeFiles/_ost_img.dir/export_point.cc.o CMakeFiles/_ost_img.dir/export_progress.cc.o CMakeFiles/_ost_img.dir/export_raster_image.cc.o CMakeFiles/_ost_img.dir/export_size.cc.o CMakeFiles/_ost_img.dir/export_mask.cc.o CMakeFiles/_ost_img.dir/export_image_list.cc.o CMakeFiles/_ost_img.dir/export_map.cc.o CMakeFiles/_ost_img.dir/wrap_img.cc.o -L/build/reproducible-path/openstructure-2.5.0/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_img.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../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/entity_view.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/clash_score.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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++/14/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/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/mol/alg/local_dist_diff_test.hh:24, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/distance_rmsd_test.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.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++/14/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/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/img/./__init__.pyc\",\"__init__.py\",doraise=True)" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 31%] Built target _ost_img -make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/depend -make[3]: Entering directory '/build/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.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/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 31%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -MF CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o.d -o CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/wrap_alg.cc -[ 31%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.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_structure_segments.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_structure_segments.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, @@ -10825,85 +10517,17 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 31%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -MF CMakeFiles/_ost_mol.dir/wrap_mol.cc.o.d -o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/wrap_mol.cc -[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.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/gfx_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_object.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.cc -[ 32%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity_property_mapper.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/alg/src/sec_structure_segments.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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: -/usr/include/c++/14/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++/14/bits/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/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_visitor.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_visitor.cc:19: -/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 32%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.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/local_dist_diff_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.cc -[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o +[ 30%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o -MF CMakeFiles/_ost_img.dir/export_map.cc.o.d -o CMakeFiles/_ost_img.dir/export_map.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_map.cc +[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.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/gfx_prim.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_prim.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_prim.cc -[ 34%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_filter.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_filter.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/auto_correlate.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/wrap_alg.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/polygon_mask.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/mask.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_mask.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 | ^~~~~~~~ @@ -10917,36 +10541,7 @@ 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/img/alg/pymod/wrap_alg.cc:25: -/usr/include/c++/14/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++/14/bits/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/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/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/gfx/src/gfx_object.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_mask.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10956,6 +10551,89 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/c++/14/string:54: +In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', + inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/14/bits/basic_string.h:904:15, + 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++/14/bits/basic_string.h:1084:16: 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] + 1084 | { 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/mol/query.hh:30: +/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++/14/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++/14/bits/basic_string.h:433:23, + 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++/14/bits/basic_string.h:882:18, + 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++/14/bits/char_traits.h:350:16: 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] + 350 | __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++/14/bits/basic_string.h:905:24: 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] + 905 | _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++/14/bits/basic_string.h:905:24: 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] + 905 | _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, @@ -10976,78 +10654,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 34%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_normalizer.cc -[ 34%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_transcendentals.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/alg/src/local_dist_diff_test.cc:4: -/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/iomanip:42, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.cc:1: -/usr/include/c++/14/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++/14/bits/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/local_dist_diff_test.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.cc:6: -/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++/14/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/gfx_test_object.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/gfx_test_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.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/editor_base.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/wrap_mol.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/wrap_mol.cc:19: -/usr/include/c++/14/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++/14/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/input.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/input.cc.o -MF CMakeFiles/ost_gfx.dir/input.cc.o.d -o CMakeFiles/ost_gfx.dir/input.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/input.cc +[ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/filter_clashes.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/filter_clashes.cc.o -MF CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o.d -o CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/filter_clashes.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, @@ -11056,52 +10664,18 @@ 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/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity_property_mapper.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity_property_mapper.cc:1: -/usr/include/c++/14/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++/14/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/prim_list.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/prim_list.cc.o -MF CMakeFiles/ost_gfx.dir/prim_list.cc.o.d -o CMakeFiles/ost_gfx.dir/prim_list.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/prim_list.cc -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.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/scene.cc.o -MF CMakeFiles/ost_gfx.dir/scene.cc.o.d -o CMakeFiles/ost_gfx.dir/scene.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.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/gfx/src/gfx_object_base.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:40, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.cc:31: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/locale:41, - from /usr/include/boost/filesystem/detail/path_traits.hpp:18, - from /usr/include/boost/filesystem/path.hpp:21, - from /usr/include/boost/filesystem/operations.hpp:20, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.cc:25: + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/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/gfx/src/gfx_object.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11111,12 +10685,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:124:31: warning: 'virtual geom::AlignedCuboid ost::gfx::GfxObj::GetBoundingBox(bool) const' was hidden [-Woverloaded-virtual=] - 124 | virtual geom::AlignedCuboid GetBoundingBox(bool use_tf=false) const; - | ^~~~~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.hh:40:31: note: by 'virtual geom::AlignedCuboid ost::gfx::GfxTestObj::GetBoundingBox() const' - 40 | virtual geom::AlignedCuboid GetBoundingBox() const; - | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/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, @@ -11124,9 +10692,7 @@ 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/gaussian.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/filter.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_filter.cc:30: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_image_list.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 | ^~~~~~~~ @@ -11140,34 +10706,7 @@ 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/img/alg/pymod/export_filter.cc:27: -/usr/include/c++/14/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++/14/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/selection.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/selection.cc.o -MF CMakeFiles/ost_gfx.dir/selection.cc.o.d -o CMakeFiles/ost_gfx.dir/selection.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/selection.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/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/prim_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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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/gfx/src/prim_list.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_image_list.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11180,46 +10719,21 @@ 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/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/obj-x86_64-linux-gnu/stage/include/ost/img/alg/transcendentals.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_transcendentals.cc: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/superpose_frames.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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_transcendentals.cc:25: -/usr/include/c++/14/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++/14/bits/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/scene.cc:40: -/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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/gfx/src/scene.cc:23: + 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/alg/src/superpose_frames.cc:20: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11232,15 +10746,11 @@ 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/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/normalizer_impl.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_normalizer.cc:30: + 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/pymod/export_editors.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 | ^~~~~~~~ @@ -11254,76 +10764,7 @@ 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/img/alg/pymod/export_normalizer.cc:27: -/usr/include/c++/14/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++/14/bits/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/gfx/src/scene.cc:49: -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:124:31: warning: 'virtual geom::AlignedCuboid ost::gfx::GfxObj::GetBoundingBox(bool) const' was hidden [-Woverloaded-virtual=] - 124 | virtual geom::AlignedCuboid GetBoundingBox(bool use_tf=false) const; - | ^~~~~~~~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.cc:50: -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.hh:40:31: note: by 'virtual geom::AlignedCuboid ost::gfx::GfxTestObj::GetBoundingBox() const' - 40 | virtual geom::AlignedCuboid GetBoundingBox() const; - | ^~~~~~~~~~~~~~ -[ 34%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_polar.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_polar.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/gfx/src/selection.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/selection.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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: -/usr/include/c++/14/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++/14/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/surface.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/surface.cc.o -MF CMakeFiles/ost_gfx.dir/surface.cc.o.d -o CMakeFiles/ost_gfx.dir/surface.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient.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/gradient.cc.o -MF CMakeFiles/ost_gfx.dir/gradient.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.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/gradient_manager.cc.o -MF CMakeFiles/ost_gfx.dir/gradient_manager.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient_manager.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient_manager.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.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/vertex_array.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.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/gfx/src/surface.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/stl_tree.h:63, - from /usr/include/c++/14/map:62, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_editors.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11333,56 +10774,52 @@ /usr/include/c++/14/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/vertex_array_helper.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/vertex_array_helper.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array_helper.cc In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object_base.hh:34, from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:40, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.cc:28: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.cc:32: /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/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/gradient.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient.hh:26: -/usr/include/c++/14/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/pymod/export_editors.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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.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/gfx_test_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.cc +[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity.cc +[ 30%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.cc.o -MF CMakeFiles/_ost_img.dir/wrap_img.cc.o.d -o CMakeFiles/_ost_img.dir/wrap_img.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/wrap_img.cc +[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/input.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/input.cc.o -MF CMakeFiles/ost_gfx.dir/input.cc.o.d -o CMakeFiles/ost_gfx.dir/input.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/input.cc +[ 31%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.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/construct_cbeta.cc.o -MF CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o.d -o CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/construct_cbeta.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/gradient_manager.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/alg/src/filter_clashes.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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/locale:41, - from /usr/include/boost/filesystem/detail/path_traits.hpp:18, - from /usr/include/boost/filesystem/path.hpp:21, - from /usr/include/boost/filesystem/operations.hpp:20, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient_manager.cc:19: + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/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/filter_clashes.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11392,15 +10829,16 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 32%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_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/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/polar.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_polar.cc:25: + 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/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_map.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 | ^~~~~~~~ @@ -11414,179 +10852,7 @@ 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/img/alg/pymod/export_polar.cc:24: -/usr/include/c++/14/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++/14/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/distance_test_common.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/distance_test_common.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_test_common.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/gfx/src/vertex_array_helper.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array_helper.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array_helper.hh:22: -/usr/include/c++/14/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++/14/bits/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/vertex_array.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /usr/include/boost/format.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc:23: -/usr/include/c++/14/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++/14/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/material.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/material.cc.o -MF CMakeFiles/ost_gfx.dir/material.cc.o.d -o CMakeFiles/ost_gfx.dir/material.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/material.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.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/povray.cc.o -MF CMakeFiles/ost_gfx.dir/povray.cc.o.d -o CMakeFiles/ost_gfx.dir/povray.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/povray.cc -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc:1311:8: warning: 'geom::Vec3 ost::gfx::{anonymous}::make_aaline_edge(const geom::Vec2&, const geom::Vec2&, float)' defined but not used [-Wunused-function] - 1311 | Vec3 make_aaline_edge(const Vec2& c1, const Vec2& c0, float s) - | ^~~~~~~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc:1239:8: warning: 'void ost::gfx::{anonymous}::render_aalines(AALineList&, float, float)' defined but not used [-Wunused-function] - 1239 | void render_aalines(AALineList& line_list, float w, float r) - | ^~~~~~~~~~~~~~ -[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.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/distance_rmsd_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.cc -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/gost_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/gost_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gost_exporter.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/texture.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/texture.cc.o -MF CMakeFiles/ost_gfx.dir/texture.cc.o.d -o CMakeFiles/ost_gfx.dir/texture.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/texture.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/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/color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/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/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/distance_test_common.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_test_common.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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++/14/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++/14/bits/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/material.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/material.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++/14/iterator:61, - from /usr/include/boost/operators.hpp:98, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:28: -/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o -cd /build/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/by_element_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_chain_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/by_chain_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_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/modules/gfx/src/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/povray.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/povray.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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/istream:40, - from /usr/include/c++/14/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/povray.cc:24: -/usr/include/c++/14/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++/14/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/superpose_frames.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/superpose_frames.cc.o -MF CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o.d -o CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/superpose_frames.cc -[ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_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/uniform_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/uniform_color_op.cc -[ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/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/gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_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/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/distance_rmsd_test.cc:2: -/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/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/distance_rmsd_test.cc:1: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_map.cc:20: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11596,180 +10862,24 @@ /usr/include/c++/14/bits/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/mol/alg/local_dist_diff_test.hh:24, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/distance_rmsd_test.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.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++/14/bits/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: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object_base.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:40, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/istream:40, - from /usr/include/c++/14/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gost_exporter.cc:24: -/usr/include/c++/14/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++/14/bits/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: -/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/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: -/usr/include/c++/14/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++/14/bits/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/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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/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++/14/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++/14/bits/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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/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++/14/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++/14/bits/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); - | ^~~~~ -[ 36%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/mol/_ost_mol.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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CMakeFiles/_ost_mol.dir/export_torsion.cc.o CMakeFiles/_ost_mol.dir/export_visitor.cc.o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -L/build/reproducible-path/openstructure-2.5.0/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_mol.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../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 -[ 36%] 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/gfx/entity.hh:29, - 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 - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: -/usr/include/c++/14/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++/14/bits/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_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); - | ^~~~~ -[ 36%] 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 -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: -/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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/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/uniform_color_op.cc:20: + from /usr/include/c++/14/locale:41, + from /usr/include/boost/filesystem/detail/path_traits.hpp:18, + from /usr/include/boost/filesystem/path.hpp:21, + from /usr/include/boost/filesystem/operations.hpp:20, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11779,6 +10889,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.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/prim_list.cc.o -MF CMakeFiles/ost_gfx.dir/prim_list.cc.o.d -o CMakeFiles/ost_gfx.dir/prim_list.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/prim_list.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, @@ -11786,17 +10898,14 @@ 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/superpose_frames.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/construct_cbeta.cc:4: /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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - 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/alg/src/superpose_frames.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/construct_cbeta.cc:1: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11806,6 +10915,18 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:124:31: warning: 'virtual geom::AlignedCuboid ost::gfx::GfxObj::GetBoundingBox(bool) const' was hidden [-Woverloaded-virtual=] + 124 | virtual geom::AlignedCuboid GetBoundingBox(bool use_tf=false) const; + | ^~~~~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.hh:40:31: note: by 'virtual geom::AlignedCuboid ost::gfx::GfxTestObj::GetBoundingBox() const' + 40 | virtual geom::AlignedCuboid GetBoundingBox() const; + | ^~~~~~~~~~~~~~ +[ 32%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o -MF CMakeFiles/_ost_mol.dir/export_property_id.cc.o.d -o CMakeFiles/_ost_mol.dir/export_property_id.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_property_id.cc +[ 32%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.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/trajectory_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/trajectory_analysis.cc +[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.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/scene.cc.o -MF CMakeFiles/ost_gfx.dir/scene.cc.o.d -o CMakeFiles/ost_gfx.dir/scene.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.cc In file included from /usr/include/c++/14/string:54: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/14/bits/basic_string.h:904:15, @@ -11816,16 +10937,16 @@ 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: + inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, + inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, + inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, + inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/14/bits/basic_string.h:1084:16: 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] 1084 | { 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/mol/query.hh:30: -/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: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ @@ -11840,14 +10961,14 @@ 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: + inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, + inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, + inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, + inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/14/bits/char_traits.h:350:16: 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] 350 | __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: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ @@ -11859,14 +10980,14 @@ 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: + inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, + inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, + inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, + inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/14/bits/basic_string.h:905:24: 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] 905 | _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: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ @@ -11878,177 +10999,23 @@ 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: + inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, + inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, + inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, + inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/14/bits/basic_string.h:905:24: 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] 905 | _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: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -[ 36%] 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 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/./__init__.pyc\",\"__init__.py\",doraise=True)" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 36%] Built target _ost_mol -make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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/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/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 36%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_sequence.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_sequence.cc.o -MF CMakeFiles/_ost_seq.dir/export_sequence.cc.o.d -o CMakeFiles/_ost_seq.dir/export_sequence.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/export_sequence.cc -[ 36%] 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 -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: -/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: -/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 36%] 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 -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/basic_gradient_color_op.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/basic_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 - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 36%] 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 -[ 36%] 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 -[ 36%] 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 -[ 36%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/filter_clashes.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/filter_clashes.cc.o -MF CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o.d -o CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/filter_clashes.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/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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/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: -/usr/include/c++/14/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++/14/bits/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/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); - | ^~~~~ 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: -/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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: -/usr/include/c++/14/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++/14/bits/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/impl/cartoon_renderer.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cartoon_renderer.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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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++/14/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++/14/bits/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/impl/entity_detail.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:19: + 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/prim_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 | ^~~~~~~~ @@ -12056,8 +11023,9 @@ from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, 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/gfx/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_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/gfx/src/prim_list.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12070,19 +11038,25 @@ 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: + 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/base/pymod/wrap_img.cc:33: /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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - 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: + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/wrap_img.cc:27: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12092,27 +11066,17 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 36%] 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 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/filter_clashes.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/trajectory_analysis.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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/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/filter_clashes.cc:19: + from /usr/include/c++/14/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/trajectory_analysis.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12122,79 +11086,15 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 32%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o -MF CMakeFiles/_ost_mol.dir/export_query.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_query.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/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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++/14/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++/14/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/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 -[ 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 -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc: In member function 'void ost::gfx::impl::CustomRenderer::PrepareRendering(ost::gfx::impl::GfxView&, ost::gfx::IndexedVertexArray&, bool)': -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:67:25: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 67 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); - | ^~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:67:54: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetFirst() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' - 67 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:68:25: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 68 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); - | ^~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:68:55: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetSecond() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' - 68 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc: In member function 'virtual void ost::gfx::impl::CustomRenderer::RenderPov(ost::gfx::PovState&, const std::string&)': -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:93:23: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 93 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); - | ^~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:93:52: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetFirst() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' - 93 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:94:23: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 94 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); - | ^~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:94:53: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetSecond() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' - 94 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -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: -/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); - | ^~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.cc:23: -/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); - | ^~~~~ -[ 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/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/pymod/export_sequence.cc:30: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity.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 | ^~~~~~~~ @@ -12208,7 +11108,7 @@ 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/seq/base/pymod/export_sequence.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12218,45 +11118,40 @@ /usr/include/c++/14/bits/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/pymod/export_sequence.cc:34: -/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++/14/bits/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/pymod/export_sequence.cc:37: -/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] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ /usr/include/c++/14/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/backbone_trace.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/backbone_trace.cc.o -MF CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/backbone_trace.cc +[ 32%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/img/_ost_img.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/img/_ost_img.so CMakeFiles/_ost_img.dir/export_data.cc.o CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o CMakeFiles/_ost_img.dir/export_extent.cc.o CMakeFiles/_ost_img.dir/export_image_handle.cc.o CMakeFiles/_ost_img.dir/export_peak.cc.o CMakeFiles/_ost_img.dir/export_phase.cc.o CMakeFiles/_ost_img.dir/export_point.cc.o CMakeFiles/_ost_img.dir/export_progress.cc.o CMakeFiles/_ost_img.dir/export_raster_image.cc.o CMakeFiles/_ost_img.dir/export_size.cc.o CMakeFiles/_ost_img.dir/export_mask.cc.o CMakeFiles/_ost_img.dir/export_image_list.cc.o CMakeFiles/_ost_img.dir/export_map.cc.o CMakeFiles/_ost_img.dir/wrap_img.cc.o -L/build/reproducible-path/openstructure-2.5.0/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_img.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../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/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/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/debug_renderer.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/debug_renderer.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity_view.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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - 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/gfx/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:26: + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity_view.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12266,32 +11161,18 @@ /usr/include/c++/14/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/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/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/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/modules/gfx/src/scene.cc:40: /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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/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/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12301,27 +11182,51 @@ /usr/include/c++/14/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/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/img/./__init__.pyc\",\"__init__.py\",doraise=True)" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 32%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.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/structure_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/structure_analysis.cc +[ 32%] Built target _ost_img +make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/depend +make[3]: Entering directory '/build/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.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/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 32%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -MF CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o.d -o CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/wrap_alg.cc +In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.cc:49: +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:124:31: warning: 'virtual geom::AlignedCuboid ost::gfx::GfxObj::GetBoundingBox(bool) const' was hidden [-Woverloaded-virtual=] + 124 | virtual geom::AlignedCuboid GetBoundingBox(bool use_tf=false) const; + | ^~~~~~~~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.cc:50: +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.hh:40:31: note: by 'virtual geom::AlignedCuboid ost::gfx::GfxTestObj::GetBoundingBox() const' + 40 | virtual geom::AlignedCuboid GetBoundingBox() const; + | ^~~~~~~~~~~~~~ +[ 34%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.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/surface.cc.o -MF CMakeFiles/ost_gfx.dir/surface.cc.o.d -o CMakeFiles/ost_gfx.dir/surface.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_filter.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_filter.cc +[ 34%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_residue.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/gfx/impl/backbone_trace.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.cc:24: + 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/gfx/src/selection.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/selection.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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/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/gfx/entity_fw.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.hh:27: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12331,24 +11236,32 @@ /usr/include/c++/14/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/gradient.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/gradient.cc.o -MF CMakeFiles/ost_gfx.dir/gradient.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient.cc +[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.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/gradient_manager.cc.o -MF CMakeFiles/ost_gfx.dir/gradient_manager.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient_manager.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient_manager.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/gfx/impl/backbone_trace.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/line_trace_renderer.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/line_trace_renderer.cc:24: + 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/pymod/export_property_id.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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - 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: + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_property_id.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12358,53 +11271,6 @@ /usr/include/c++/14/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/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/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/impl/simple_renderer.cc:26: -/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); - | ^~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc: In member function 'void ost::gfx::impl::SimpleRenderer::PrepareRendering(ost::gfx::impl::GfxView&, ost::gfx::IndexedVertexArray&)': -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:125:25: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 125 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); - | ^~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:125:54: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetFirst() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' - 125 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:126:25: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 126 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); - | ^~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:126:55: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetSecond() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' - 126 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc: In member function 'virtual void ost::gfx::impl::SimpleRenderer::RenderPov(ost::gfx::PovState&, const std::string&)': -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:203:23: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 203 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); - | ^~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:203:52: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetFirst() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' - 203 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:204:23: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 204 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); - | ^~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:204:53: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetSecond() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' - 204 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -[ 37%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/img/alg/_ost_img_alg.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img_alg.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/img/alg/_ost_img_alg.so CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -L/build/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_img_alg.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/x86_64-linux-gnu/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 -[ 37%] 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 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/img/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 37%] Built target _ost_img_alg -[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/tabulated_trig.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/tabulated_trig.cc.o -MF CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/tabulated_trig.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, @@ -12412,7 +11278,7 @@ 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/gfx/src/impl/backbone_trace.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/structure_analysis.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 | ^~~~~~~~ @@ -12420,8 +11286,7 @@ from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, 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: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/structure_analysis.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12431,33 +11296,18 @@ /usr/include/c++/14/bits/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/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/gfx.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/backbone_trace.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/backbone_trace.cc:22: -/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); - | ^~~~~~~~ -[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/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/trace_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/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/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/connect_renderer_base.cc:23: + 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/gradient.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/stl_tree.h:63, - from /usr/include/c++/14/map:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: + from /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient.hh:26: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12467,21 +11317,26 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 39%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.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/construct_cbeta.cc.o -MF CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o.d -o CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/construct_cbeta.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/trace_renderer_base.cc:24: + 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/pymod/export_query.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/stl_tree.h:63, - from /usr/include/c++/14/map:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_query.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12491,110 +11346,23 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/c++/14/string:54: -In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', - inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/14/bits/basic_string.h:904:15, - 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 = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, - inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, - inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, - inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: -/usr/include/c++/14/bits/basic_string.h:1084:16: 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] - 1084 | { 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/mol/query.hh:30: -/usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [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++/14/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++/14/bits/basic_string.h:433:23, - 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++/14/bits/basic_string.h:882:18, - inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, - inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, - inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, - inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, - inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, - inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, - inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, - inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, - inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, - inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, - inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: -/usr/include/c++/14/bits/char_traits.h:350:16: 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] - 350 | __c1 = __c2; - | ^~~~ -/usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [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 = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, - inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, - inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, - inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: -/usr/include/c++/14/bits/basic_string.h:905:24: 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] - 905 | _M_capacity(__str._M_allocated_capacity); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::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 = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, - inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, - inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, - inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: -/usr/include/c++/14/bits/basic_string.h:905:24: 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] - 905 | _M_capacity(__str._M_allocated_capacity); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]': -/usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here - 2107 | variant temp(rhs); - | ^~~~ -[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/fast_spheres.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/fast_spheres.cc.o -MF CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/fast_spheres.cc -[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/render_options.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/render_options/render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/render_options.cc -[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.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/render_options/line_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/line_render_options.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/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/mapped_property.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/gfx/src/gradient_manager.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:28: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/locale:41, + from /usr/include/boost/filesystem/detail/path_traits.hpp:18, + from /usr/include/boost/filesystem/path.hpp:21, + from /usr/include/boost/filesystem/operations.hpp:20, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient_manager.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12607,14 +11375,18 @@ 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/gfx/entity.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/trace_renderer.cc:24: + 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/gfx/src/surface.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: + from /usr/include/c++/14/bits/stl_tree.h:63, + from /usr/include/c++/14/map:62, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12624,21 +11396,46 @@ /usr/include/c++/14/bits/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/gfx/src/gfx_object_base.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:40, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.cc:28: +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] + 55 | virtual void DeepSwap(GfxNode& n); + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' + 58 | virtual void DeepSwap(GfxObj& go); + | ^~~~~~~~ +[ 35%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_normalizer.cc +[ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_residue_view.cc +[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.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/consistency_checks.cc.o -MF CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o.d -o CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/consistency_checks.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/alg/src/construct_cbeta.cc:4: + 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/auto_correlate.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/wrap_alg.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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/construct_cbeta.cc:1: + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/wrap_alg.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12648,25 +11445,32 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.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/render_options/custom_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/custom_render_options.cc -[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.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/render_options/cpk_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/cpk_render_options.cc +[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.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/vertex_array.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.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/entity.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/render_options.cc:23: + 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/gaussian.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/filter.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_filter.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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - 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/gfx/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/input.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/render_options.cc:22: + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_filter.cc:27: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12679,16 +11483,25 @@ 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/fast_spheres.cc: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/pymod/export_residue.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/stl_tree.h:63, - from /usr/include/c++/14/map:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_residue.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12698,47 +11511,26 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.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/render_options/simple_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/simple_render_options.cc -[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.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/render_options/sline_render_options.cc.o -MF 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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/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/trajectory_analysis.cc -[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -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/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/line_trace_render_options.cc -[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.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 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/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/cartoon_render_options.cc -[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/trace_render_options.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/render_options/trace_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/trace_render_options.cc -[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/map_handle_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 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modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/map_handle_color_op.cc -[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.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 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-MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_s.cc -[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.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/map_iso_gen_o.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_o.cc -[ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.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/structure_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/structure_analysis.cc -[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_octree.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/map_octree.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_octree.cc -[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/octree_isocont.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/octree_isocont.cc.o -MF CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/octree_isocont.cc +[ 35%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_transcendentals.cc +[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.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/pdbize.cc.o -MF CMakeFiles/ost_mol_alg.dir/pdbize.cc.o.d -o CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/pdbize.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/alg/src/trajectory_analysis.cc:27: + 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: /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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /usr/include/c++/14/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/trajectory_analysis.cc:23: + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/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: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12748,21 +11540,21 @@ /usr/include/c++/14/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/vertex_array_helper.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/vertex_array_helper.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array_helper.cc +[ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o -MF CMakeFiles/_ost_mol.dir/export_surface.cc.o.d -o CMakeFiles/_ost_mol.dir/export_surface.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_surface.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/vertex_array.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_iso_prop.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_o.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array_helper.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array_helper.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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/memory:66, - from /usr/include/boost/smart_ptr/shared_array.hpp:21, - from /usr/include/boost/shared_array.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_o.cc:21: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array_helper.hh:22: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12775,14 +11567,15 @@ 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/map_handle_color_op.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: + from /usr/include/boost/format.hpp:17, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12795,18 +11588,20 @@ 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/gfx/src/impl/map_iso_gen.cc: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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen.cc:23: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12816,6 +11611,14 @@ /usr/include/c++/14/bits/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++/14/bits/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, @@ -12824,16 +11627,24 @@ 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/gfx/src/impl/map_iso_gen_s.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/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_normalizer.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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/memory:66, - from /usr/include/boost/smart_ptr/shared_array.hpp:21, - from /usr/include/boost/shared_array.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_s.cc:21: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_normalizer.cc:27: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12843,6 +11654,14 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 35%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_polar.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_polar.cc +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc:1311:8: warning: 'geom::Vec3 ost::gfx::{anonymous}::make_aaline_edge(const geom::Vec2&, const geom::Vec2&, float)' defined but not used [-Wunused-function] + 1311 | Vec3 make_aaline_edge(const Vec2& c1, const Vec2& c0, float s) + | ^~~~~~~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc:1239:8: warning: 'void ost::gfx::{anonymous}::render_aalines(AALineList&, float, float)' defined but not used [-Wunused-function] + 1239 | void render_aalines(AALineList& line_list, float w, float r) + | ^~~~~~~~~~~~~~ In file included from /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, @@ -12850,15 +11669,21 @@ 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/structure_analysis.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_residue_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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - 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 /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_residue_view.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12868,21 +11693,32 @@ /usr/include/c++/14/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/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 +[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/material.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/material.cc.o -MF CMakeFiles/ost_gfx.dir/material.cc.o.d -o CMakeFiles/ost_gfx.dir/material.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/material.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/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/map_slab.cc:26: + 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/obj-x86_64-linux-gnu/stage/include/ost/img/alg/transcendentals.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_transcendentals.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/map_slab.cc:22: + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_transcendentals.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12892,25 +11728,22 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -MF CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bounding_box.cc +[ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_query_view_wrapper.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/image.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/discrete_shrink.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/map_iso.cc:27: + 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/material.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/material.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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/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/gfx/src/map_iso.cc:23: +In file included from /usr/include/c++/14/iterator:61, + from /usr/include/boost/operators.hpp:98, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:28: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12920,27 +11753,25 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.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/consistency_checks.cc.o -MF CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o.d -o CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/consistency_checks.cc +[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.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/povray.cc.o -MF CMakeFiles/ost_gfx.dir/povray.cc.o.d -o CMakeFiles/ost_gfx.dir/povray.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/povray.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/image_handle.hh:38, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/octree_isocont.cc:24: + 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++/14/iterator:61, - from /usr/include/boost/container_hash/is_range.hpp:16, - from /usr/include/boost/container_hash/hash.hpp:15, - from /usr/include/boost/functional/hash.hpp:6, - from /usr/include/boost/unordered/unordered_map.hpp:20, - from /usr/include/boost/unordered_map.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:25: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12953,23 +11784,23 @@ 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/image_handle.hh:38, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_octree.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_octree.cc:24: + 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/pymod/export_surface.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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/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/image_handle.hh:32: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_surface.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12979,89 +11810,39 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.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/pdbize.cc.o -MF CMakeFiles/ost_mol_alg.dir/pdbize.cc.o.d -o CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/pdbize.cc -In file included from /usr/include/eigen3/Eigen/Core:341, - from /usr/include/eigen3/Eigen/QR:11, - from /usr/include/eigen3/Eigen/SVD:11, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cartoon_renderer.cc:26: -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] - 327 | internal::triangular_matrix_vector_product - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 328 | - | ~~~~~~~~~ - 332 | ::run(actualLhs.rows(),actualLhs.cols(), - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 333 | actualLhs.data(),actualLhs.outerStride(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 334 | actualRhsPtr,1, - | ~~~~~~~~~~~~~~~ - 335 | dest.data(),dest.innerStride(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 336 | actualAlpha); - | ~~~~~~~~~~~~ -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const float*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]' declared here - 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 41%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -MF CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o.d -o CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/export_profile_handle.cc -[ 41%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -MF CMakeFiles/_ost_seq.dir/wrap_seq.cc.o.d -o CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/wrap_seq.cc -[ 41%] 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 -[ 41%] 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 -[ 41%] 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 -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: -/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/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: -/usr/include/c++/14/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/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++/14/bits/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/modules/mol/alg/src/pdbize.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/pdbize.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/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/polar.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_polar.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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - 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: + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_polar.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13071,31 +11852,27 @@ /usr/include/c++/14/bits/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++/14/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/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 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: + 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/povray.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/povray.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/istream:40, + from /usr/include/c++/14/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/povray.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13105,10 +11882,10 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o +[ 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 -[ 41%] 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/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o -MF CMakeFiles/_ost_mol.dir/export_torsion.cc.o.d -o CMakeFiles/_ost_mol.dir/export_torsion.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_torsion.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, @@ -13139,46 +11916,66 @@ | ^~~~~~~~ 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: + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/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 -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{ - | ^~~~~~~~ +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/base/pymod/export_bounding_box.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bounding_box.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 43%] 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 +/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o -MF CMakeFiles/_ost_mol.dir/export_visitor.cc.o.d -o CMakeFiles/_ost_mol.dir/export_visitor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_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/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: + 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/base/pymod/export_query_view_wrapper.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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/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: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_query_view_wrapper.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13188,8 +11985,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 43%] 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/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, @@ -13308,14 +12103,22 @@ 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: + 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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:22: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13325,6 +12128,10 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -MF CMakeFiles/_ost_mol.dir/wrap_mol.cc.o.d -o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/wrap_mol.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 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: @@ -13334,91 +12141,8 @@ /usr/include/c++/14/bits/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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 43%] 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 -[ 43%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.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/entity_to_density.cc.o -MF CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o.d -o CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/entity_to_density.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/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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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++/14/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++/14/bits/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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/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: -/usr/include/c++/14/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++/14/bits/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/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::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++/14/bits/basic_string.h:904:15, 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, @@ -13668,6 +12392,253 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ +[ 36%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.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/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity_property_mapper.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/pymod/export_visitor.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_visitor.cc:19: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 36%] 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 +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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/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++/14/bits/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/editor_base.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/wrap_mol.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/wrap_mol.cc:19: +/usr/include/c++/14/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++/14/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 +[ 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 +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/texture.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/texture.cc.o -MF CMakeFiles/ost_gfx.dir/texture.cc.o.d -o CMakeFiles/ost_gfx.dir/texture.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/texture.cc +[ 37%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/img/alg/_ost_img_alg.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img_alg.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/img/alg/_ost_img_alg.so CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -L/build/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_img_alg.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/x86_64-linux-gnu/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 +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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/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++/14/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++/14/bits/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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/istream:40, + from /usr/include/c++/14/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gost_exporter.cc:24: +/usr/include/c++/14/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++/14/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/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/img/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 37%] Built target _ost_img_alg +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/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/color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/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/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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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: +/usr/include/c++/14/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++/14/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 +[ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.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/entity_to_density.cc.o -MF CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o.d -o CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/entity_to_density.cc +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/domain_find.cc:11: +In member function 'void ost::mol::alg::AdjacencyBitmap::set(size_t, size_t, bool, bool)', + inlined from 'ost::mol::alg::AdjacencyBitmap::AdjacencyBitmap(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, int, int)' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:49:16, + inlined from 'static ost::mol::alg::DomainsPtr ost::mol::alg::Domains::FromDistMats(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, Real, int, bool, bool)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/domain_find.cc:363:37: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:109:23: warning: '*(uint64_t*)' may be used uninitialized [-Wmaybe-uninitialized] + 109 | data_[byte_index] &= ~(one << bit_index); + | ~~~~~~~~~~~~~~~~^ +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/by_element_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_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/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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_chain_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/by_chain_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.cc +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 struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/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: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/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/gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_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, @@ -13698,6 +12669,67 @@ 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/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity_property_mapper.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity_property_mapper.cc:1: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/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: +/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++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/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++/14/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++/14/bits/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, @@ -13724,13 +12756,78 @@ /usr/include/c++/14/bits/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/alg/src/domain_find.cc:11: -In member function 'void ost::mol::alg::AdjacencyBitmap::set(size_t, size_t, bool, bool)', - inlined from 'ost::mol::alg::AdjacencyBitmap::AdjacencyBitmap(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, int, int)' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:49:16, - inlined from 'static ost::mol::alg::DomainsPtr ost::mol::alg::Domains::FromDistMats(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, Real, int, bool, bool)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/domain_find.cc:363:37: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:109:23: warning: '*(uint64_t*)' may be used uninitialized [-Wmaybe-uninitialized] - 109 | data_[byte_index] &= ~(one << bit_index); - | ~~~~~~~~~~~~~~~~^ +[ 39%] 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 +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/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: +/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++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/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/uniform_color_op.cc:20: +/usr/include/c++/14/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++/14/bits/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/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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/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++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/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 +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 /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, @@ -13823,6 +12920,28 @@ /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/gfx/entity.hh:29, + 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 + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/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 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++/14/bits/basic_string.h:904:15, 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, @@ -14238,14 +13357,531 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -[ 43%] Linking CXX shared library ../../../stage/lib/libost_gfx.so -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/test_texture.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/textures/test_texture.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/glyph_texture.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/textures/glyph_texture.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gfx.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_gfx.so.2.5 -o ../../../stage/lib/libost_gfx.so.2.5.0 CMakeFiles/ost_gfx.dir/bitmap_io.cc.o CMakeFiles/ost_gfx.dir/exporter.cc.o CMakeFiles/ost_gfx.dir/collada_exporter.cc.o CMakeFiles/ost_gfx.dir/color.cc.o CMakeFiles/ost_gfx.dir/primitives.cc.o CMakeFiles/ost_gfx.dir/entity.cc.o CMakeFiles/ost_gfx.dir/symmetry_node.cc.o CMakeFiles/ost_gfx.dir/gfx_node.cc.o 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CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o CMakeFiles/ost_gfx.dir/map_iso.cc.o CMakeFiles/ost_gfx.dir/map_slab.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -L/build/reproducible-path/openstructure-2.5.0/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_conop.so.2.5.0 ../../../stage/lib/libost_img_alg.so.2.5.0 /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so ../../../stage/lib/libost_db.so.2.5.0 ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img.so.2.5.0 ../../../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 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_gfx.so.2.5.0 ../../../stage/lib/libost_gfx.so.2.5 ../../../stage/lib/libost_gfx.so +[ 39%] 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 +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/basic_gradient_color_op.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/basic_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 + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/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++/14/bits/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/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 + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/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 +[ 39%] 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/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); + | ^~~~~ +[ 39%] 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 +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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/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++/14/bits/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++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/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: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/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 +[ 40%] 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 +[ 40%] 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 +[ 40%] 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_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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.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/backbone_trace.cc.o -MF CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/backbone_trace.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/gfx/src/impl/cartoon_renderer.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cartoon_renderer.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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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++/14/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++/14/bits/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/impl/entity_detail.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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/gfx/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:22: +/usr/include/c++/14/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++/14/bits/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/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 + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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: +/usr/include/c++/14/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++/14/bits/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: +/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); + | ^~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.cc:23: +/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); + | ^~~~~ +[ 40%] 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 +[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.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/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: +/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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/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: +/usr/include/c++/14/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++/14/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/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, + 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/gfx/impl/backbone_trace.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.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++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/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/gfx/entity_fw.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.hh:27: +/usr/include/c++/14/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++/14/bits/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/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/debug_renderer.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/debug_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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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/gfx/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:26: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc: In member function 'void ost::gfx::impl::CustomRenderer::PrepareRendering(ost::gfx::impl::GfxView&, ost::gfx::IndexedVertexArray&, bool)': +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:67:25: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 67 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); + | ^~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:67:54: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetFirst() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' + 67 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:68:25: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 68 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); + | ^~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:68:55: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetSecond() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' + 68 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc: In member function 'virtual void ost::gfx::impl::CustomRenderer::RenderPov(ost::gfx::PovState&, const std::string&)': +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:93:23: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 93 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); + | ^~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:93:52: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetFirst() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' + 93 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:94:23: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 94 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); + | ^~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:94:53: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetSecond() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' + 94 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +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/gfx/src/impl/backbone_trace.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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: +/usr/include/c++/14/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++/14/bits/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/impl/simple_renderer.cc:26: +/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); + | ^~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc: In member function 'void ost::gfx::impl::SimpleRenderer::PrepareRendering(ost::gfx::impl::GfxView&, ost::gfx::IndexedVertexArray&)': +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:125:25: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 125 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); + | ^~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:125:54: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetFirst() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' + 125 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:126:25: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 126 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); + | ^~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:126:55: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetSecond() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' + 126 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +[ 40%] 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 +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc: In member function 'virtual void ost::gfx::impl::SimpleRenderer::RenderPov(ost::gfx::PovState&, const std::string&)': +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:203:23: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 203 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); + | ^~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:203:52: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetFirst() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' + 203 | const geom::Vec3& p0=it->bond.GetFirst().GetPos(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:204:23: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 204 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); + | ^~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:204:53: note: the temporary was destroyed at the end of the full expression 'ost::mol::BondHandle::GetSecond() const().ost::mol::AtomHandle::ost::mol::AtomBase.ost::mol::AtomBase::GetPos()' + 204 | const geom::Vec3& p2=it->bond.GetSecond().GetPos(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +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/gfx/impl/backbone_trace.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/line_trace_renderer.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/line_trace_renderer.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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++/14/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++/14/bits/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/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/gfx.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/backbone_trace.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/backbone_trace.cc:22: +/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/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); + | ^~~~~~~~ +[ 40%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/mol/_ost_mol.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/mol/_ost_mol.so CMakeFiles/_ost_mol.dir/export_atom.cc.o CMakeFiles/_ost_mol.dir/export_atom_view.cc.o CMakeFiles/_ost_mol.dir/export_bond.cc.o CMakeFiles/_ost_mol.dir/export_chain.cc.o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o CMakeFiles/_ost_mol.dir/export_editors.cc.o CMakeFiles/_ost_mol.dir/export_entity.cc.o CMakeFiles/_ost_mol.dir/export_entity_view.cc.o CMakeFiles/_ost_mol.dir/export_property_id.cc.o CMakeFiles/_ost_mol.dir/export_query.cc.o CMakeFiles/_ost_mol.dir/export_residue.cc.o CMakeFiles/_ost_mol.dir/export_residue_view.cc.o CMakeFiles/_ost_mol.dir/export_surface.cc.o CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o CMakeFiles/_ost_mol.dir/export_torsion.cc.o CMakeFiles/_ost_mol.dir/export_visitor.cc.o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -L/build/reproducible-path/openstructure-2.5.0/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_mol.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../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 +[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/tabulated_trig.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/tabulated_trig.cc.o -MF CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/tabulated_trig.cc +[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/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/trace_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/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/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/connect_renderer_base.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/stl_tree.h:63, + from /usr/include/c++/14/map:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/fast_spheres.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/fast_spheres.cc.o -MF CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/fast_spheres.cc +[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/render_options.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/render_options/render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/render_options.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/./__init__.pyc\",\"__init__.py\",doraise=True)" +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.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/render_options/line_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/line_render_options.cc +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.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/render_options/custom_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/custom_render_options.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/trace_renderer_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 + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/stl_tree.h:63, + from /usr/include/c++/14/map:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 41%] Built target _ost_mol +make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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/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/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 43%] Built target ost_gfx +make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 41%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_sequence.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_sequence.cc.o -MF CMakeFiles/_ost_seq.dir/export_sequence.cc.o.d -o CMakeFiles/_ost_seq.dir/export_sequence.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/export_sequence.cc In file included from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, @@ -14340,11 +13976,131 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -[ 43%] Linking CXX shared library ../../../../stage/lib/libost_mol_alg.so +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/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/mapped_property.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:28: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.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/render_options/cpk_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/cpk_render_options.cc +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.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/render_options/simple_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/simple_render_options.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/entity.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/trace_renderer.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o +cd /build/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/render_options/sline_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/sline_render_options.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/fast_spheres.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/stl_tree.h:63, + from /usr/include/c++/14/map:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.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/render_options/line_trace_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/line_trace_render_options.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/entity.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/render_options.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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/gfx/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/input.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/render_options.cc:22: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.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/render_options/cartoon_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/cartoon_render_options.cc +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/trace_render_options.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/render_options/trace_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/trace_render_options.cc +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/map_handle_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/map_handle_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/map_handle_color_op.cc +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.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/map_iso.cc.o -MF CMakeFiles/ost_gfx.dir/map_iso.cc.o.d -o CMakeFiles/ost_gfx.dir/map_iso.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/map_iso.cc +[ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_slab.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/map_slab.cc.o -MF CMakeFiles/ost_gfx.dir/map_slab.cc.o.d -o CMakeFiles/ost_gfx.dir/map_slab.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/map_slab.cc +[ 41%] Linking CXX shared library ../../../../stage/lib/libost_mol_alg.so 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/atom_scattering_properties.txt /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/atom_scattering_properties.txt 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/stereo_chemical_props.txt /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/stereo_chemical_props.txt cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol_alg.so.2.5 -o ../../../../stage/lib/libost_mol_alg.so.2.5.0 CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o CMakeFiles/ost_mol_alg.dir/clash_score.cc.o CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o CMakeFiles/ost_mol_alg.dir/pdbize.cc.o CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o CMakeFiles/ost_mol_alg.dir/domain_find.cc.o CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o CMakeFiles/ost_mol_alg.dir/accessibility.cc.o CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o CMakeFiles/ost_mol_alg.dir/molck.cc.o CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -L/build/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_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_conop.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5.0 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_db.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../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 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../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/libsqlite3.so +[ 43%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen.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/map_iso_gen.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen.cc +[ 43%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.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/map_iso_gen_s.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_s.cc +[ 43%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.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 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modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_octree.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/map_octree.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_octree.cc +[ 43%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG 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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/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -MF CMakeFiles/_ost_seq.dir/wrap_seq.cc.o.d -o CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/wrap_seq.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol_alg.so.2.5.0 ../../../../stage/lib/libost_mol_alg.so.2.5 ../../../../stage/lib/libost_mol_alg.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 43%] Built target ost_mol_alg @@ -14355,83 +14111,35 @@ make -f modules/io/src/CMakeFiles/ost_io.dir/build.make modules/io/src/CMakeFiles/ost_io.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_manager.cc.o -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_utils.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/io_utils.cc.o -MF CMakeFiles/ost_io.dir/io_utils.cc.o.d -o CMakeFiles/ost_io.dir/io_utils.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/io_utils.cc -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/convert.cc.o -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o -[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include 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-isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_reader.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK 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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/io/src/CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_reader.cc -[ 44%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/seq/_ost_seq.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_seq.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/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/seq/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/seq/./__init__.pyc\",\"__init__.py\",doraise=True)" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 44%] Built target _ost_seq -make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 44%] Building CXX object modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_bindings_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o -MF CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o.d -o CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/export_tmalign.cc -[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o -MF CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o.d -o CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_writer.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/io/seq/sequence_io_handler.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/io_manager.cc:19: -/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{ - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:22: +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/vertex_array.hh:34, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_iso_prop.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_o.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++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/memory:66, + from /usr/include/boost/smart_ptr/shared_array.hpp:21, + from /usr/include/boost/shared_array.hpp:17, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_o.cc:21: /usr/include/c++/14/bits/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/io/mol/pdb_reader.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pdb_handler.cc:35: -/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{ - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pdb_handler.cc:22: +/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++/14/bits/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/io/src/mol/entity_io_pqr_handler.cc:35: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen.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 | ^~~~~~~~ @@ -14442,7 +14150,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pqr_handler.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14455,22 +14163,14 @@ 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/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/io/src/mol/entity_io_crd_handler.cc:33: + 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/map_handle_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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_crd_handler.cc:22: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14480,11 +14180,16 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 43%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/octree_isocont.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/octree_isocont.cc.o -MF CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/octree_isocont.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/io/mol/mmcif_reader.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mmcif_handler.cc:35: + 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/obj-x86_64-linux-gnu/stage/include/ost/img/alg/discrete_shrink.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/map_iso.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 | ^~~~~~~~ @@ -14494,8 +14199,8 @@ from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mmcif_handler.cc:22: + 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/gfx/src/map_iso.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14508,18 +14213,50 @@ 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/io/src/mol/pdb_writer.cc:35: + 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/gfx/src/impl/map_iso_gen_s.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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/locale:41, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_writer.cc:22: +In file included from /usr/include/c++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/memory:66, + from /usr/include/boost/smart_ptr/shared_array.hpp:21, + from /usr/include/boost/shared_array.hpp:17, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_s.cc:21: +/usr/include/c++/14/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++/14/bits/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/pymod/export_sequence.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/export_sequence.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14530,13 +14267,92 @@ 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/io/mol/mmcif_reader.hh:25: + 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/pymod/export_sequence.cc:34: /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++/14/bits/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/pymod/export_sequence.cc:37: +/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++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/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/image_handle.hh:32: +/usr/include/c++/14/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++/14/bits/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.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/map_slab.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/map_slab.cc:22: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/convert.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/convert.cc.o -MF CMakeFiles/ost_io.dir/convert.cc.o.d -o CMakeFiles/ost_io.dir/convert.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/convert.cc +[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_utils.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/io_utils.cc.o -MF CMakeFiles/ost_io.dir/io_utils.cc.o.d -o CMakeFiles/ost_io.dir/io_utils.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/io_utils.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/io/seq/sequence_io_handler.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/io_manager.cc:19: +/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{ + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:22: +/usr/include/c++/14/bits/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, @@ -14557,22 +14373,75 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pqr_handler.cc: In constructor 'ost::io::PQRReader::PQRReader(const boost::filesystem::path&)': -/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pqr_handler.cc:61:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] - 61 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pqr_handler.cc:28: -/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here - 29 | inline std::string extension(const path& p) - | ^~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_crd_handler.cc: In constructor 'ost::io::CRDReader::CRDReader(const boost::filesystem::path&)': -/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_crd_handler.cc:63:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] - 63 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_crd_handler.cc:27: -/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here - 29 | inline std::string extension(const path& p) - | ^~~~~~~~~ +[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_crd_handler.cc +[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pqr_handler.cc +[ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mae_handler.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/image_handle.hh:38, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/octree_isocont.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++/14/iterator:61, + from /usr/include/boost/container_hash/is_range.hpp:16, + from /usr/include/boost/container_hash/hash.hpp:15, + from /usr/include/boost/functional/hash.hpp:6, + from /usr/include/boost/unordered/unordered_map.hpp:20, + from /usr/include/boost/unordered_map.hpp:17, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:25: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_reader.cc +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pdb_handler.cc +In file included from /usr/include/eigen3/Eigen/Core:341, + from /usr/include/eigen3/Eigen/QR:11, + from /usr/include/eigen3/Eigen/SVD:11, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cartoon_renderer.cc:26: +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] + 327 | internal::triangular_matrix_vector_product + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 328 | + | ~~~~~~~~~ + 332 | ::run(actualLhs.rows(),actualLhs.cols(), + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 333 | actualLhs.data(),actualLhs.outerStride(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 334 | actualRhsPtr,1, + | ~~~~~~~~~~~~~~~ + 335 | dest.data(),dest.innerStride(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 336 | actualAlpha); + | ~~~~~~~~~~~~ +/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const float*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]' declared here + 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_writer.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, @@ -14580,8 +14449,7 @@ 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/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_sdf_handler.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pqr_handler.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 | ^~~~~~~~ @@ -14591,8 +14459,8 @@ from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/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/io/src/mol/entity_io_sdf_handler.cc:23: + from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pqr_handler.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14602,17 +14470,35 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_sdf_handler.cc +/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pqr_handler.cc: In constructor 'ost::io::PQRReader::PQRReader(const boost::filesystem::path&)': +/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pqr_handler.cc:61:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] + 61 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pqr_handler.cc:28: +/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here + 29 | inline std::string extension(const path& p) + | ^~~~~~~~~ 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/sequence_list.hh:24: + 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/io/src/mol/entity_io_crd_handler.cc:33: /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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_crd_handler.cc:22: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14622,6 +14508,14 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_crd_handler.cc: In constructor 'ost::io::CRDReader::CRDReader(const boost::filesystem::path&)': +/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_crd_handler.cc:63:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] + 63 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_crd_handler.cc:27: +/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here + 29 | inline std::string extension(const path& p) + | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/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, @@ -14650,29 +14544,70 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pdb_handler.cc: In member function 'virtual void ost::io::EntityIOPDBHandler::Export(const ost::mol::EntityView&, const boost::filesystem::path&) const': -/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pdb_handler.cc:52:50: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] - 52 | if (boost::iequals(boost::filesystem::extension(loc), ".pqr")) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pdb_handler.cc:27: +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mmcif_handler.cc +/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mae_handler.cc: In constructor 'ost::io::MAEReader::MAEReader(const boost::filesystem::path&)': +/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mae_handler.cc:60:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] + 60 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mae_handler.cc:31: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ +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/io/mol/pdb_reader.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pdb_handler.cc:35: +/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{ + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pdb_handler.cc:22: +/usr/include/c++/14/bits/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/io/src/mol/pdb_reader.cc:32: + 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/io/src/mol/pdb_writer.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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/locale:41, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_writer.cc:22: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_reader.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_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/sequence_list.hh: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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /usr/include/boost/iostreams/filter/gzip.hpp:21, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_reader.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14709,14 +14644,38 @@ /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mae_handler.cc: In constructor 'ost::io::MAEReader::MAEReader(const boost::filesystem::path&)': -/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mae_handler.cc:60:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] - 60 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mae_handler.cc:31: +/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pdb_handler.cc: In member function 'virtual void ost::io::EntityIOPDBHandler::Export(const ost::mol::EntityView&, const boost::filesystem::path&) const': +/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pdb_handler.cc:52:50: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] + 52 | if (boost::iequals(boost::filesystem::extension(loc), ".pqr")) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pdb_handler.cc:27: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/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/io/src/mol/pdb_reader.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /usr/include/boost/iostreams/filter/gzip.hpp:21, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_reader.cc:19: +/usr/include/c++/14/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++/14/bits/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/io/src/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_reader.cc:35: @@ -14747,16 +14706,19 @@ 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/io/src/mol/sdf_reader.cc:29: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_sdf_handler.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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /usr/include/boost/algorithm/string/std/string_traits.hpp:15, - from /usr/include/boost/algorithm/string/std_containers_traits.hpp:19, - from /usr/include/boost/algorithm/string.hpp:18, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_reader.cc:23: + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/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/io/src/mol/entity_io_sdf_handler.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14766,27 +14728,11 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_reader.cc: In member function 'void ost::io::SDFReader::ClearState(const boost::filesystem::path&)': -/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_reader.cc:108:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] - 108 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_reader.cc:24: -/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here - 29 | inline std::string extension(const path& p) - | ^~~~~~~~~ -[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/save_entity.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/save_entity.cc.o -MF CMakeFiles/ost_io.dir/mol/save_entity.cc.o.d -o CMakeFiles/ost_io.dir/mol/save_entity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/save_entity.cc -[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/load_entity.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/load_entity.cc.o -MF CMakeFiles/ost_io.dir/mol/load_entity.cc.o.d -o CMakeFiles/ost_io.dir/mol/load_entity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/load_entity.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/conop/conop.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_writer.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_writer.cc:23: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mmcif_handler.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 | ^~~~~~~~ @@ -14797,7 +14743,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_writer.hh:25: + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mmcif_handler.cc:22: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14808,20 +14754,10 @@ 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/io/seq/sequence_io_handler.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/save_entity.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.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{ | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/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/io/src/mol/save_entity.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14830,25 +14766,18 @@ 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/bindings/wrap_tmalign.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/export_tmalign.cc:22: + 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/io/src/mol/sdf_reader.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/export_tmalign.cc:20: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/boost/algorithm/string/std/string_traits.hpp:15, + from /usr/include/boost/algorithm/string/std_containers_traits.hpp:19, + from /usr/include/boost/algorithm/string.hpp:18, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_reader.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14858,11 +14787,33 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o -MF CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o.d -o CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_writer.cc +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/save_entity.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/save_entity.cc.o -MF CMakeFiles/ost_io.dir/mol/save_entity.cc.o.d -o CMakeFiles/ost_io.dir/mol/save_entity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/save_entity.cc +/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_reader.cc: In member function 'void ost::io::SDFReader::ClearState(const boost::filesystem::path&)': +/build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_reader.cc:108:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] + 108 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_reader.cc:24: +/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here + 29 | inline std::string extension(const path& p) + | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/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/io/seq/sequence_io_handler.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/save_entity.cc:20: /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{ | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/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/io/src/mol/save_entity.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14893,7 +14844,8 @@ 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/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/io/src/mol/load_entity.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_writer.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_writer.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 | ^~~~~~~~ @@ -14903,8 +14855,8 @@ from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/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/io/src/mol/load_entity.cc:19: + from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_writer.hh:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -14914,26 +14866,12 @@ /usr/include/c++/14/bits/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/io/seq/sequence_io_handler.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/load_entity.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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/load_entity.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/load_entity.cc.o -MF CMakeFiles/ost_io.dir/mol/load_entity.cc.o.d -o CMakeFiles/ost_io.dir/mol/load_entity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/load_entity.cc [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/surface_io_msms_handler.cc [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/load_surface.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/load_surface.cc.o -MF CMakeFiles/ost_io.dir/mol/load_surface.cc.o.d -o CMakeFiles/ost_io.dir/mol/load_surface.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/load_surface.cc -[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -MF CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o.d -o CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/chemdict_parser.cc -[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/io_profile.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/io_profile.cc.o -MF CMakeFiles/ost_io.dir/mol/io_profile.cc.o.d -o CMakeFiles/ost_io.dir/mol/io_profile.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/io_profile.cc -[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -MF CMakeFiles/ost_io.dir/mol/dcd_io.cc.o.d -o CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/dcd_io.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, @@ -14973,6 +14911,48 @@ /usr/include/boost/filesystem/convenience.hpp:41:13: note: declared here 41 | inline path change_extension(const path& p, const path& new_extension) | ^~~~~~~~~~~~~~~~ +[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -MF CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o.d -o CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/chemdict_parser.cc +[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/io_profile.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/io_profile.cc.o -MF CMakeFiles/ost_io.dir/mol/io_profile.cc.o.d -o CMakeFiles/ost_io.dir/mol/io_profile.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/io_profile.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/conop/conop.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/load_entity.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++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/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/io/src/mol/load_entity.cc:19: +/usr/include/c++/14/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++/14/bits/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/io/seq/sequence_io_handler.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/load_entity.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++/14/bits/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, @@ -15009,8 +14989,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/star_parser.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/star_parser.cc.o -MF CMakeFiles/ost_io.dir/mol/star_parser.cc.o.d -o CMakeFiles/ost_io.dir/mol/star_parser.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/star_parser.cc +[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -MF CMakeFiles/ost_io.dir/mol/dcd_io.cc.o.d -o CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/dcd_io.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, @@ -15039,6 +15019,13 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 45%] Linking CXX shared library ../../../stage/lib/libost_gfx.so +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/test_texture.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/textures/test_texture.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/glyph_texture.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/textures/glyph_texture.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gfx.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o CMakeFiles/ost_gfx.dir/map_iso.cc.o CMakeFiles/ost_gfx.dir/map_slab.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -L/build/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_conop.so.2.5.0 ../../../stage/lib/libost_img_alg.so.2.5.0 /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so ../../../stage/lib/libost_db.so.2.5.0 ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img.so.2.5.0 ../../../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 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so +[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/star_parser.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/star_parser.cc.o -MF CMakeFiles/ost_io.dir/mol/star_parser.cc.o.d -o CMakeFiles/ost_io.dir/mol/star_parser.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/star_parser.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, @@ -15068,14 +15055,19 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 45%] Building CXX object modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_bindings_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o -MF CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o.d -o CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/wrap_bindings.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_gfx.so.2.5.0 ../../../stage/lib/libost_gfx.so.2.5 ../../../stage/lib/libost_gfx.so +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 45%] Built target ost_gfx [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_reader.cc +[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_str.cc.o [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o -MF CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o.d -o CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_info.cc -[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_str.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_str.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_str.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_str.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_str.cc +[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_str.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_str.cc.o -MF CMakeFiles/ost_io.dir/mol/sdf_str.cc.o.d -o CMakeFiles/ost_io.dir/mol/sdf_str.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_str.cc +[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_str.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_str.cc.o -MF CMakeFiles/ost_io.dir/mol/mmcif_str.cc.o.d -o CMakeFiles/ost_io.dir/mol/mmcif_str.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_str.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, @@ -15104,10 +15096,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_str.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_str.cc.o -MF CMakeFiles/ost_io.dir/mol/sdf_str.cc.o.d -o CMakeFiles/ost_io.dir/mol/sdf_str.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_str.cc -[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_str.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_str.cc.o -MF CMakeFiles/ost_io.dir/mol/mmcif_str.cc.o.d -o CMakeFiles/ost_io.dir/mol/mmcif_str.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_str.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/modules/io/src/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/dcd_io.cc:40: @@ -15135,26 +15123,6 @@ 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/sequence_list.hh: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 - | ^~~~~~~~ -/usr/include/c++/14/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++/14/bits/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/io/src/mol/mmcif_reader.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] @@ -15176,17 +15144,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/stereochemical_params_reader.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/io/mol/mmcif_reader.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_reader.cc: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++/14/bits/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, @@ -15215,14 +15172,32 @@ /usr/include/c++/14/bits/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/io/mol/mmcif_reader.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_reader.cc: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++/14/bits/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/io/mol/pdb_reader.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_str.cc:22: +/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++/14/bits/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/io/mol/mmcif_str.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_str.cc:20: + 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/io/mol/sdf_str.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_str.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 | ^~~~~~~~ @@ -15233,7 +15208,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_str.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_str.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15243,21 +15218,23 @@ /usr/include/c++/14/bits/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/io/mmcif_reader.hh:25, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_str.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{ - | ^~~~~~~~ +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/sequence_list.hh: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 + | ^~~~~~~~ /usr/include/c++/14/bits/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/io/mol/pdb_reader.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_str.cc:22: -/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{ - | ^~~~~~~~ +/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15266,9 +15243,9 @@ 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/entity_view.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_str.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_str.cc:20: + 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/io/mol/mmcif_str.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_str.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 | ^~~~~~~~ @@ -15279,7 +15256,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_str.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_str.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15289,9 +15266,21 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 45%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/bindings/_ost_bindings.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_bindings.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/bindings/_ost_bindings.so CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o CMakeFiles/_ost_bindings.dir/wrap_bindings.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_bindings.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../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/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mmcif_reader.hh:25, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_str.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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/stereochemical_params_reader.cc +[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o -MF CMakeFiles/ost_io.dir/mol/omf.cc.o.d -o CMakeFiles/ost_io.dir/mol/omf.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/omf.cc +[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/clustal_io_handler.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, @@ -15330,59 +15319,16 @@ /usr/include/c++/14/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/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./__init__.pyc\",\"__init__.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./lga.pyc\",\"lga.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./hbplus.pyc\",\"hbplus.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./msms.pyc\",\"msms.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./tmtools.pyc\",\"tmtools.py\",doraise=True)" -[ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o -MF CMakeFiles/ost_io.dir/mol/omf.cc.o.d -o CMakeFiles/ost_io.dir/mol/omf.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/omf.cc -[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./dssp.pyc\",\"dssp.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/clustal_io_handler.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./clustalw.pyc\",\"clustalw.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./utils.pyc\",\"utils.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./naccess.pyc\",\"naccess.py\",doraise=True)" [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/load.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/load.cc.o -MF CMakeFiles/ost_io.dir/seq/load.cc.o.d -o CMakeFiles/ost_io.dir/seq/load.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/load.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./hhblits.pyc\",\"hhblits.py\",doraise=True)" [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/save.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/save.cc.o -MF CMakeFiles/ost_io.dir/seq/save.cc.o.d -o CMakeFiles/ost_io.dir/seq/save.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/save.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./hhblits2.pyc\",\"hhblits2.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./hhblits3.pyc\",\"hhblits3.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./blast.pyc\",\"blast.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./cadscore.pyc\",\"cadscore.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./kclust.pyc\",\"kclust.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./ialign.pyc\",\"ialign.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./mmseqs2.pyc\",\"mmseqs2.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./dockq.pyc\",\"dockq.py\",doraise=True)" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 46%] Built target _ost_bindings -make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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/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.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 46%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/export_linear_db.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_db_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/pymod/CMakeFiles/_ost_db.dir/export_linear_db.cc.o -MF CMakeFiles/_ost_db.dir/export_linear_db.cc.o.d -o CMakeFiles/_ost_db.dir/export_linear_db.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/pymod/export_linear_db.cc [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/fasta_io_handler.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/modules/io/src/seq/load.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/load.cc:19: -/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{ - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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/io/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/load.hh:26: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pir_io_handler.cc +[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/promod_io_handler.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, @@ -15409,39 +15355,18 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pir_io_handler.cc -[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/promod_io_handler.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/io/seq/sequence_io_handler.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/save.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/load.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/load.cc:19: /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{ | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/istream:40, - from /usr/include/c++/14/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/save.cc:19: -/usr/include/c++/14/bits/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/sequence_list.hh: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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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/io/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/load.hh:26: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15455,14 +15380,6 @@ /usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/hhm_io_handler.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, @@ -15483,6 +15400,26 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/hhm_io_handler.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/io/seq/sequence_io_handler.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/save.cc:22: +/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{ + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/istream:40, + from /usr/include/c++/14/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/save.cc:19: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/omf.cc: In function 'void {anonymous}::DumpName(std::ostream&, const String&)': /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/omf.cc:816:43: warning: the address of 'static constexpr unsigned char std::numeric_limits::max()' will never be NULL [-Waddress] 816 | ss << std::numeric_limits::max << ". "; @@ -15515,34 +15452,6 @@ /usr/include/c++/14/bits/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/io/src/seq/sequence_io_handler.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/clustal_io_handler.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/clustal_io_handler.cc: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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pssm_io_handler.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/modules/io/src/seq/sequence_io_handler.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/fasta_io_handler.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/fasta_io_handler.cc:19: -/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{ - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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/io/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/fasta_io_handler.hh:24: -/usr/include/c++/14/bits/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, @@ -15563,12 +15472,10 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/load_map.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/load_map.cc.o -MF CMakeFiles/ost_io.dir/img/load_map.cc.o.d -o CMakeFiles/ost_io.dir/img/load_map.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/load_map.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/modules/io/src/seq/sequence_io_handler.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pir_io_handler.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pir_io_handler.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/fasta_io_handler.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/fasta_io_handler.cc:19: /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{ | ^~~~~~~~ @@ -15577,38 +15484,22 @@ from /usr/include/c++/14/cmath:3898, 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/io/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pir_io_handler.hh:24: + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/fasta_io_handler.hh:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/hhm_io_handler.cc: In member function 'virtual void ost::io::HhmIOHandler::Import(ost::seq::ProfileHandle&, const boost::filesystem::path&)': -/build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/hhm_io_handler.cc:133:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] - 133 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/hhm_io_handler.cc:27: -/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here - 29 | inline std::string extension(const path& p) - | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/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/io/seq/sequence_io_handler.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/promod_io_handler.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/promod_io_handler.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/sequence_io_handler.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/clustal_io_handler.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/clustal_io_handler.cc: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{ | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/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/io/seq/sequence_io_handler.hh:22: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dx_handler.cc +[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pssm_io_handler.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, @@ -15629,6 +15520,22 @@ /usr/include/c++/14/bits/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/io/src/seq/sequence_io_handler.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pir_io_handler.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pir_io_handler.cc:19: +/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{ + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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/io/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pir_io_handler.hh:24: +/usr/include/c++/14/bits/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, @@ -15649,8 +15556,28 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_spi_handler.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/io/seq/sequence_io_handler.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/promod_io_handler.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/promod_io_handler.cc:22: +/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{ + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/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/io/seq/sequence_io_handler.hh:22: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/load_map.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/load_map.cc.o -MF CMakeFiles/ost_io.dir/img/load_map.cc.o.d -o CMakeFiles/ost_io.dir/img/load_map.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/load_map.cc +[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dx_handler.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, @@ -15658,22 +15585,10 @@ 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/db/extract_data_helper.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/db/pymod/export_linear_db.cc:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh: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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/db/pymod/export_linear_db.cc:21: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15683,15 +15598,16 @@ /usr/include/c++/14/bits/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_spi_handler.cc +/build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/hhm_io_handler.cc: In member function 'virtual void ost::io::HhmIOHandler::Import(ost::seq::ProfileHandle&, const boost::filesystem::path&)': +/build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/hhm_io_handler.cc:133:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] + 133 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/hhm_io_handler.cc:27: +/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here + 29 | inline std::string extension(const path& p) + | ^~~~~~~~~ /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pssm_io_handler.cc: In member function 'virtual void ost::io::PssmIOHandler::Import(ost::seq::ProfileHandle&, const boost::filesystem::path&)': /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pssm_io_handler.cc:47:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 47 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { @@ -15730,16 +15646,8 @@ /usr/include/c++/14/bits/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/io/seq/sequence_io_handler.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/load_map.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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_mrc_handler.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, @@ -15768,6 +15676,22 @@ /usr/include/c++/14/bits/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/io/seq/sequence_io_handler.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/load_map.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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dm3_handler.cc +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_tiff_handler.cc +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dat_handler.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, @@ -15800,16 +15724,19 @@ /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_mrc_handler.cc +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_ipl_handler.cc +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_jpk_handler.cc +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_nanoscope_handler.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/image.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_situs_handler.cc:34: + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dm3_handler.cc:37: /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 | ^~~~~~~~ @@ -15817,8 +15744,10 @@ from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/iomanip:42, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_situs_handler.cc:26: + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dm3_handler.cc:27: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15828,36 +15757,22 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dm3_handler.cc -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_tiff_handler.cc -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dat_handler.cc -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_ipl_handler.cc -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_jpk_handler.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/io/src/img/map_io_tiff_handler.cc: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/io/src/img/map_io_dat_handler.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++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/istream:40, - from /usr/include/c++/14/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_tiff_handler.cc:26: +In file included from /usr/include/c++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/memory:66, + from /usr/include/boost/smart_ptr/shared_array.hpp:21, + from /usr/include/boost/shared_array.hpp:17, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dat_handler.cc:21: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15873,7 +15788,8 @@ 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/io/src/img/map_io_dm3_handler.cc:37: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_situs_handler.cc:34: /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 | ^~~~~~~~ @@ -15881,10 +15797,8 @@ from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dm3_handler.cc:27: + from /usr/include/c++/14/iomanip:42, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_situs_handler.cc:26: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15894,24 +15808,26 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_nanoscope_handler.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/image.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dat_handler.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/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_tiff_handler.cc:33: /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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/memory:66, - from /usr/include/boost/smart_ptr/shared_array.hpp:21, - from /usr/include/boost/shared_array.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dat_handler.cc:21: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/istream:40, + from /usr/include/c++/14/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_tiff_handler.cc:26: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15954,18 +15870,19 @@ 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/io/src/img/map_io_ipl_handler.cc:31: + 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/alg_transform.hh:24, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/transform.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_jpk_handler.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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/iomanip:42, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_ipl_handler.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_jpk_handler.cc:22: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -15979,19 +15896,18 @@ 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/obj-x86_64-linux-gnu/stage/include/ost/img/alg/alg_transform.hh:24, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/transform.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_jpk_handler.cc:24: + 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/io/src/img/map_io_ipl_handler.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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_jpk_handler.cc:22: + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/iomanip:42, + from /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_ipl_handler.cc:22: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -16001,10 +15917,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_png_handler.cc -[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_df3_handler.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, @@ -16035,12 +15947,38 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 48%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_db_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o -MF CMakeFiles/_ost_db.dir/wrap_db.cc.o.d -o CMakeFiles/_ost_db.dir/wrap_db.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/pymod/wrap_db.cc +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_png_handler.cc +[ 48%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/seq/_ost_seq.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_seq.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/seq/_ost_seq.so CMakeFiles/_ost_seq.dir/export_sequence.cc.o CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -L/build/reproducible-path/openstructure-2.5.0/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 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../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 +[ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_df3_handler.cc [ 49%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/image_format.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/image_format.cc.o -MF CMakeFiles/ost_io.dir/img/image_format.cc.o.d -o CMakeFiles/ost_io.dir/img/image_format.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/image_format.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/seq/./__init__.pyc\",\"__init__.py\",doraise=True)" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 49%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/tiff_util.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/tiff_util.cc.o -MF CMakeFiles/ost_io.dir/img/tiff_util.cc.o.d -o CMakeFiles/ost_io.dir/img/tiff_util.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/tiff_util.cc +[ 49%] Built target _ost_seq +make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 49%] Building CXX object modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_bindings_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o -MF CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o.d -o CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/export_tmalign.cc +make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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" 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modules/db/pymod/CMakeFiles/_ost_db.dir/export_linear_db.cc.o -MF CMakeFiles/_ost_db.dir/export_linear_db.cc.o.d -o CMakeFiles/_ost_db.dir/export_linear_db.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/pymod/export_linear_db.cc +[ 49%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_db_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o -MF CMakeFiles/_ost_db.dir/wrap_db.cc.o.d -o CMakeFiles/_ost_db.dir/wrap_db.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/pymod/wrap_db.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, @@ -16071,6 +16009,16 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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.dir/DependInfo.cmake "--color=" +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.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 49%] Building CXX object modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -MF CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o.d -o CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/wrap_seq_alg.cc +[ 49%] Building CXX object modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_bindings_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o -MF CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o.d -o CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/wrap_bindings.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, @@ -16097,14 +16045,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/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.dir/DependInfo.cmake "--color=" -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.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 49%] Building CXX object modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -MF CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o.d -o CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/wrap_seq_alg.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, @@ -16131,34 +16071,88 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 49%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/db/_ost_db.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod && /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 -o ../../../stage/lib/python3.12/dist-packages/ost/db/_ost_db.so CMakeFiles/_ost_db.dir/export_linear_db.cc.o CMakeFiles/_ost_db.dir/wrap_db.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_db.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/x86_64-linux-gnu/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 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/db/./__init__.pyc\",\"__init__.py\",doraise=True)" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 49%] Built target _ost_db -make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.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/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.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_processor.cc.o -[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_compound.cc.o -[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/wrap_conop.cc.o -[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_conop.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/wrap_conop.cc.o -MF CMakeFiles/_ost_conop.dir/wrap_conop.cc.o.d -o CMakeFiles/_ost_conop.dir/wrap_conop.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/wrap_conop.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/export_compound.cc.o -MF CMakeFiles/_ost_conop.dir/export_compound.cc.o.d -o CMakeFiles/_ost_conop.dir/export_compound.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_compound.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/export_processor.cc.o -MF CMakeFiles/_ost_conop.dir/export_processor.cc.o.d -o CMakeFiles/_ost_conop.dir/export_processor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_processor.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -MF CMakeFiles/_ost_conop.dir/export_heuristic.cc.o.d -o CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_heuristic.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -MF CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o.d -o CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_amino_acids.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/export_conop.cc.o -MF CMakeFiles/_ost_conop.dir/export_conop.cc.o.d -o CMakeFiles/_ost_conop.dir/export_conop.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_conop.cc -[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_diag.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/export_diag.cc.o -MF CMakeFiles/_ost_conop.dir/export_diag.cc.o.d -o CMakeFiles/_ost_conop.dir/export_diag.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_diag.cc -[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_rule_based.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/export_rule_based.cc.o -MF CMakeFiles/_ost_conop.dir/export_rule_based.cc.o.d -o CMakeFiles/_ost_conop.dir/export_rule_based.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_rule_based.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_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/pymod/export_tmalign.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/export_tmalign.cc:20: +/usr/include/c++/14/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++/14/bits/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++/14/bits/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/db/extract_data_helper.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/db/pymod/export_linear_db.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/db/pymod/export_linear_db.cc:21: +/usr/include/c++/14/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++/14/bits/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++/14/bits/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, @@ -16209,7 +16203,58 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 49%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/bindings/_ost_bindings.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_bindings.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/bindings/_ost_bindings.so CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o CMakeFiles/_ost_bindings.dir/wrap_bindings.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_bindings.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../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 +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./__init__.pyc\",\"__init__.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./lga.pyc\",\"lga.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./hbplus.pyc\",\"hbplus.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./msms.pyc\",\"msms.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./tmtools.pyc\",\"tmtools.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./dssp.pyc\",\"dssp.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./clustalw.pyc\",\"clustalw.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./utils.pyc\",\"utils.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./naccess.pyc\",\"naccess.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./hhblits.pyc\",\"hhblits.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./hhblits2.pyc\",\"hhblits2.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./hhblits3.pyc\",\"hhblits3.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./blast.pyc\",\"blast.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./cadscore.pyc\",\"cadscore.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./kclust.pyc\",\"kclust.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./ialign.pyc\",\"ialign.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./mmseqs2.pyc\",\"mmseqs2.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/bindings/./dockq.pyc\",\"dockq.py\",doraise=True)" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 49%] Built target _ost_bindings +[ 49%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/db/_ost_db.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod && /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 -o ../../../stage/lib/python3.12/dist-packages/ost/db/_ost_db.so CMakeFiles/_ost_db.dir/export_linear_db.cc.o CMakeFiles/_ost_db.dir/wrap_db.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_db.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/x86_64-linux-gnu/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 +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/db/./__init__.pyc\",\"__init__.py\",doraise=True)" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 49%] Built target _ost_db +make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.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/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.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 49%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_compound.cc.o +[ 49%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/wrap_conop.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/export_compound.cc.o -MF CMakeFiles/_ost_conop.dir/export_compound.cc.o.d -o CMakeFiles/_ost_conop.dir/export_compound.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_compound.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/wrap_conop.cc.o -MF CMakeFiles/_ost_conop.dir/wrap_conop.cc.o.d -o CMakeFiles/_ost_conop.dir/wrap_conop.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/wrap_conop.cc +[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_processor.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/export_processor.cc.o -MF CMakeFiles/_ost_conop.dir/export_processor.cc.o.d -o CMakeFiles/_ost_conop.dir/export_processor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_processor.cc +[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -MF CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o.d -o CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_amino_acids.cc +[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_conop.cc.o +[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_heuristic.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/export_conop.cc.o -MF CMakeFiles/_ost_conop.dir/export_conop.cc.o.d -o CMakeFiles/_ost_conop.dir/export_conop.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_conop.cc +[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_diag.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/export_diag.cc.o -MF CMakeFiles/_ost_conop.dir/export_diag.cc.o.d -o CMakeFiles/_ost_conop.dir/export_diag.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_diag.cc +[ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_rule_based.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -MF CMakeFiles/_ost_conop.dir/export_heuristic.cc.o.d -o CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_heuristic.cc [ 50%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/export_rule_based.cc.o -MF CMakeFiles/_ost_conop.dir/export_rule_based.cc.o.d -o CMakeFiles/_ost_conop.dir/export_rule_based.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_rule_based.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -MF CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o.d -o CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_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, @@ -16217,8 +16262,8 @@ 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/heuristic.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_heuristic.cc:23: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/processor.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_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 | ^~~~~~~~ @@ -16232,7 +16277,7 @@ 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/conop/pymod/export_heuristic.cc:21: + from /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_processor.cc:20: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -16278,20 +16323,9 @@ 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/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_amino_acids.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 /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/processor.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_processor.cc:21: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/rule_based.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_rule_based.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 | ^~~~~~~~ @@ -16305,7 +16339,7 @@ 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/conop/pymod/export_processor.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_rule_based.cc:20: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -16315,6 +16349,17 @@ /usr/include/c++/14/bits/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_handle.hh:25, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/diag.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_diag.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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, @@ -16325,7 +16370,7 @@ 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/conop/pymod/export_amino_acids.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_diag.cc:20: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -16335,21 +16380,14 @@ /usr/include/c++/14/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/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -16363,7 +16401,7 @@ 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/conop/pymod/export_compound.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_heuristic.cc:21: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -16379,8 +16417,8 @@ 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/obj-x86_64-linux-gnu/stage/include/ost/conop/diag.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_diag.cc:21: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_amino_acids.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 | ^~~~~~~~ @@ -16394,7 +16432,7 @@ 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/conop/pymod/export_diag.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_amino_acids.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -16404,14 +16442,21 @@ /usr/include/c++/14/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/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -16425,7 +16470,7 @@ 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/conop/pymod/export_rule_based.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/export_compound.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -16476,77 +16521,77 @@ make -f modules/gui/src/CMakeFiles/ost_gui.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/depend make -f modules/io/tests/CMakeFiles/test_mae_standalone.dir/build.make modules/io/tests/CMakeFiles/test_mae_standalone.dir/depend make -f modules/mol/alg/src/CMakeFiles/lddt.dir/build.make modules/mol/alg/src/CMakeFiles/lddt.dir/depend +make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.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/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.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/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/chemdict_tool.dir/DependInfo.cmake "--color=" -make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/depend -make -f tools/molck/CMakeFiles/molck.dir/build.make tools/molck/CMakeFiles/molck.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/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/lddt.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/io/tests /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/tests /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/tests/CMakeFiles/test_mae_standalone.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/tools/molck /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/tools/molck /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/tools/molck/CMakeFiles/molck.dir/DependInfo.cmake "--color=" +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.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.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/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.dir/DependInfo.cmake "--color=" +[ 50%] Generating tools/moc_tool_options_win.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp_parameters +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/mol/alg/src/CMakeFiles/lddt.dir/build.make modules/mol/alg/src/CMakeFiles/lddt.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/conop/src/CMakeFiles/chemdict_tool.dir/build.make modules/conop/src/CMakeFiles/chemdict_tool.dir/build -[ 50%] Generating data_viewer/moc_argand.cpp -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' -[ 50%] Generating data_viewer/moc_fft_panel.cpp -[ 50%] Generating tools/moc_tool_options_win.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp_parameters -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/io/tests/CMakeFiles/test_mae_standalone.dir/build.make modules/io/tests/CMakeFiles/test_mae_standalone.dir/build -make -f modules/mol/alg/src/CMakeFiles/lddt.dir/build.make modules/mol/alg/src/CMakeFiles/lddt.dir/build -[ 50%] Generating data_viewer/moc_data_viewer_panel_base.cpp -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/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp_parameters -make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.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/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp_parameters +[ 50%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/forcefield.cc.o make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f tools/molck/CMakeFiles/molck.dir/build.make tools/molck/CMakeFiles/molck.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/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp_parameters -[ 50%] Generating data_viewer/moc_data_viewer.cpp -[ 50%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/forcefield.cc.o -[ 50%] Building CXX object modules/io/tests/CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp_parameters -[ 50%] Building CXX object modules/mol/alg/src/CMakeFiles/lddt.dir/lddt.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/forcefield.cc.o -MF CMakeFiles/ost_mol_mm.dir/forcefield.cc.o.d -o CMakeFiles/ost_mol_mm.dir/forcefield.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/forcefield.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_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 -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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/io/tests/CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o -MF CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o.d -o CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/tests/test_mae_standalone.cc -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 -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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/mol/alg/src/CMakeFiles/lddt.dir/lddt.cc.o -MF CMakeFiles/lddt.dir/lddt.cc.o.d -o CMakeFiles/lddt.dir/lddt.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/lddt.cc -[ 51%] Building CXX object tools/molck/CMakeFiles/molck.dir/main.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/tools/molck && /usr/bin/c++ -DBOOST_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 -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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 tools/molck/CMakeFiles/molck.dir/main.cc.o -MF CMakeFiles/molck.dir/main.cc.o.d -o CMakeFiles/molck.dir/main.cc.o -c /build/reproducible-path/openstructure-2.5.0/tools/molck/main.cc -[ 51%] Building CXX object modules/conop/src/CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o +[ 50%] Building CXX object modules/conop/src/CMakeFiles/chemdict_tool.dir/chemdict_tool.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_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 -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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/conop/src/CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o -MF CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o.d -o CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/chemdict_tool.cc -[ 51%] Generating data_viewer/moc_info_panel.cpp -[ 51%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp_parameters +[ 50%] Building CXX object modules/mol/alg/src/CMakeFiles/lddt.dir/lddt.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 -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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/mol/alg/src/CMakeFiles/lddt.dir/lddt.cc.o -MF CMakeFiles/lddt.dir/lddt.cc.o.d -o CMakeFiles/lddt.dir/lddt.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/lddt.cc +[ 50%] Building CXX object modules/io/tests/CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_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 -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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/io/tests/CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o -MF CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o.d -o CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/tests/test_mae_standalone.cc +[ 50%] Generating data_viewer/moc_argand.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp_parameters +[ 50%] Generating data_viewer/moc_data_viewer.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp_parameters +[ 50%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o -MF CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o.d -o CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/ff_reader.cc -[ 51%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o +[ 50%] Generating data_viewer/moc_data_viewer_panel_base.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp_parameters +[ 50%] Generating data_viewer/moc_fft_panel.cpp +[ 50%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o -MF CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o.d -o CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/buildingblock.cc -[ 51%] Generating data_viewer/moc_null_overlay.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp_parameters +[ 50%] Generating data_viewer/moc_info_panel.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp_parameters +[ 50%] Generating data_viewer/moc_null_overlay.cpp cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_null_overlay.cpp_parameters -[ 53%] Generating data_viewer/moc_overlay_base.cpp +[ 51%] Generating data_viewer/moc_overlay_base.cpp cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_base.cpp_parameters -[ 53%] Generating data_viewer/moc_overlay_manager_gui.cpp +[ 51%] Generating data_viewer/moc_overlay_manager_gui.cpp cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_manager_gui.cpp_parameters -[ 53%] Generating data_viewer/moc_pointlist_overlay_base.cpp +[ 51%] Generating data_viewer/moc_pointlist_overlay_base.cpp cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp_parameters +make -f tools/molck/CMakeFiles/molck.dir/build.make tools/molck/CMakeFiles/molck.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/tools/molck /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/tools/molck /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/tools/molck/CMakeFiles/molck.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f tools/molck/CMakeFiles/molck.dir/build.make tools/molck/CMakeFiles/molck.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 53%] Building CXX object tools/molck/CMakeFiles/molck.dir/main.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/tools/molck && /usr/bin/c++ -DBOOST_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 -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -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 tools/molck/CMakeFiles/molck.dir/main.cc.o -MF CMakeFiles/molck.dir/main.cc.o.d -o CMakeFiles/molck.dir/main.cc.o -c /build/reproducible-path/openstructure-2.5.0/tools/molck/main.cc [ 53%] Generating messages/moc_log_reader.cpp cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/messages && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_log_reader.cpp_parameters +[ 53%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/gromacs_block_modifiers.cc [ 53%] Generating messages/moc_message_box_widget.cpp cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/messages && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_message_box_widget.cpp_parameters [ 53%] Generating messages/moc_message_widget.cpp cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/messages && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_message_widget.cpp_parameters -[ 53%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o [ 53%] Generating moc_dock_widget.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/gromacs_block_modifiers.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_dock_widget.cpp_parameters [ 53%] Generating moc_file_browser.cpp cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp_parameters @@ -16570,32 +16615,6 @@ cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_perspective.cpp_parameters [ 54%] Generating moc_scene_menu.cpp cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_menu.cpp_parameters -[ 54%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/conop/_ost_conop.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_conop.dir/link.txt --verbose=1 -[ 54%] Generating moc_scene_selection.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp_parameters -/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/python3.12/dist-packages/ost/conop/_ost_conop.so CMakeFiles/_ost_conop.dir/wrap_conop.cc.o CMakeFiles/_ost_conop.dir/export_compound.cc.o CMakeFiles/_ost_conop.dir/export_processor.cc.o CMakeFiles/_ost_conop.dir/export_heuristic.cc.o CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o CMakeFiles/_ost_conop.dir/export_conop.cc.o CMakeFiles/_ost_conop.dir/export_diag.cc.o CMakeFiles/_ost_conop.dir/export_rule_based.cc.o CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -L/build/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_conop.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../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 -[ 54%] Generating moc_widget.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_widget.cpp_parameters -[ 54%] Generating moc_widget_geom_handler.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_geom_handler.cpp_parameters -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/conop/./__init__.pyc\",\"__init__.py\",doraise=True)" -[ 54%] Generating moc_widget_pool.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_pool.cpp_parameters -[ 54%] Generating panels/moc_bottom_bar.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_bottom_bar.cpp_parameters -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/conop/./cleanup.pyc\",\"cleanup.py\",doraise=True)" -[ 54%] Generating panels/moc_button_bar.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_bar.cpp_parameters -[ 54%] Generating panels/moc_drop_box.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp_parameters -[ 54%] Generating panels/moc_button_box.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_box.cpp_parameters -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 54%] Generating panels/moc_event_button.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_event_button.cpp_parameters -[ 54%] Generating panels/moc_panel_bar.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_bar.cpp_parameters 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, @@ -16625,6 +16644,31 @@ 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/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/forcefield.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/vector:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:23: +/usr/include/c++/14/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++/14/bits/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/io/tests/test_mae_standalone.cc:2: @@ -16648,26 +16692,22 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 54%] Built target _ost_conop -make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.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.dir/DependInfo.cmake "--color=" +[ 54%] Generating moc_scene_selection.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp_parameters 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/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/forcefield.cc:20: + 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/lddt.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:23: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/iomanip:42, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/lddt.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -16677,13 +16717,57 @@ /usr/include/c++/14/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' -make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 54%] Generating moc_widget.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_widget.cpp_parameters +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/mol/alg/local_dist_diff_test.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/lddt.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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 54%] Generating moc_widget_geom_handler.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_geom_handler.cpp_parameters +[ 54%] Generating moc_widget_pool.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_pool.cpp_parameters +[ 54%] Generating panels/moc_bottom_bar.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_bottom_bar.cpp_parameters +[ 54%] Generating panels/moc_button_bar.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_bar.cpp_parameters +[ 54%] Generating panels/moc_button_box.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_box.cpp_parameters +[ 54%] Generating panels/moc_drop_box.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp_parameters +[ 54%] Generating panels/moc_event_button.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_event_button.cpp_parameters +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/lddt.cc:39: +/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 struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/14/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/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_scene.cc.o -MF CMakeFiles/_ost_gfx.dir/export_scene.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_scene.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_scene.cc -[ 55%] Generating panels/moc_panel_manager.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_manager.cpp_parameters -[ 55%] Generating panels/moc_panel_widget_container.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_widget_container.cpp_parameters -[ 55%] Generating panels/moc_side_bar.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_side_bar.cpp_parameters -[ 55%] Generating panels/moc_splitter_panel_bar.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_splitter_panel_bar.cpp_parameters -[ 55%] Generating panels/moc_tabbed_panel_bar.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_tabbed_panel_bar.cpp_parameters -[ 55%] Generating python_shell/moc_completer_base.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp_parameters +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_bar_widget_holder.cpp_parameters 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/lddt.cc:30: + 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/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/chemdict_tool.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 | ^~~~~~~~ @@ -16738,8 +16814,10 @@ from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/iomanip:42, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/lddt.cc:19: + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/chemdict_tool.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -16749,8 +16827,47 @@ /usr/include/c++/14/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/chemdict_tool.cc: In function 'int main(int, const char**)': +/build/reproducible-path/openstructure-2.5.0/modules/conop/src/chemdict_tool.cc:69:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] + 69 | if (boost::iequals(".gz", boost::filesystem::extension(argv[2]))) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/chemdict_tool.cc:27: +/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here + 29 | inline std::string extension(const path& p) + | ^~~~~~~~~ +[ 55%] Generating panels/moc_panel_manager.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_manager.cpp_parameters +[ 55%] Generating panels/moc_panel_widget_container.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_widget_container.cpp_parameters +[ 55%] Generating panels/moc_side_bar.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_side_bar.cpp_parameters +[ 55%] Generating panels/moc_splitter_panel_bar.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_splitter_panel_bar.cpp_parameters +[ 55%] Generating panels/moc_tabbed_panel_bar.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_tabbed_panel_bar.cpp_parameters +[ 55%] Generating python_shell/moc_completer_base.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp_parameters +[ 55%] Linking CXX executable ../../../stage/bin/test_mae_standalone +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mae_standalone.dir/link.txt --verbose=1 [ 56%] Generating python_shell/moc_gutter.cpp cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_gutter.cpp_parameters +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o -o ../../../stage/bin/test_mae_standalone -L/build/reproducible-path/openstructure-2.5.0/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_io.so.2.5.0 ../../../stage/lib/libost_mol_alg.so.2.5.0 ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_img_alg.so.2.5.0 ../../../stage/lib/libost_img.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 ../../../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/libQt5Xml.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.13 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.13 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so +[ 56%] Generating python_shell/moc_main_thread_runner.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_main_thread_runner.cpp_parameters +[ 56%] Generating python_shell/moc_output_redirector.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_output_redirector.cpp_parameters +[ 56%] Generating python_shell/moc_path_completer.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_path_completer.cpp_parameters +[ 56%] Generating python_shell/moc_python_completer.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_completer.cpp_parameters +[ 56%] Generating python_shell/moc_python_interpreter.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp_parameters +[ 56%] Generating python_shell/moc_python_interpreter_worker.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter_worker.cpp_parameters +[ 56%] Generating python_shell/moc_python_namespace_tree_model.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_namespace_tree_model.cpp_parameters +[ 56%] Generating python_shell/moc_python_shell.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell.cpp_parameters 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, @@ -16762,19 +16879,6 @@ /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/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/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/chemdict_tool.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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/boost/program_options/errors.hpp:12, @@ -16784,53 +16888,30 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/chemdict_tool.cc:24: -/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 56%] Generating python_shell/moc_python_shell_widget.cpp /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++/14/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/chemdict_tool.cc: In function 'int main(int, const char**)': -/build/reproducible-path/openstructure-2.5.0/modules/conop/src/chemdict_tool.cc:69:57: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] - 69 | if (boost::iequals(".gz", boost::filesystem::extension(argv[2]))) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/chemdict_tool.cc:27: -/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here - 29 | inline std::string extension(const path& p) - | ^~~~~~~~~ -[ 56%] Generating python_shell/moc_main_thread_runner.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_main_thread_runner.cpp_parameters -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/mol/alg/local_dist_diff_test.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/lddt.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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 56%] Generating python_shell/moc_output_redirector.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_output_redirector.cpp_parameters -[ 56%] Generating python_shell/moc_path_completer.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_path_completer.cpp_parameters +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp_parameters +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 58%] Generating python_shell/moc_state.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_state.cpp_parameters +[ 58%] Built target test_mae_standalone +[ 58%] Generating python_shell/moc_state_machine.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_state_machine.cpp_parameters +[ 58%] Generating python_shell/moc_text_logger.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp_parameters +[ 58%] Generating python_shell/moc_transition_guard.cpp +[ 58%] Generating python_shell/moc_transition.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_transition_guard.cpp_parameters +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_transition.cpp_parameters +[ 58%] Generating scene_win/moc_context_menu.cpp +[ 58%] Generating scene_win/moc_current_selection_node.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp_parameters +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp_parameters 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/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.5.0/tools/molck/main.cc:10: @@ -16871,32 +16952,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 56%] Generating python_shell/moc_python_completer.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_completer.cpp_parameters -In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/lddt.cc:39: -/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 struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/wrap_gfx.cc:19: -/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 58%] Generating scene_win/moc_entity_part_node.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp_parameters -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/gfx_object_base.hh:26, - 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/modules/gfx/pymod/export_scene.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_scene.cc:19: -/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 58%] Generating scene_win/moc_gfx_scene_node.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_gfx_scene_node.cpp_parameters -[ 58%] Generating scene_win/moc_label_node.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_label_node.cpp_parameters -[ 59%] Generating scene_win/moc_render_mode_node.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp_parameters -[ 60%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/seq/alg/_ost_seq_alg.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_seq_alg.dir/link.txt --verbose=1 -[ 60%] Generating scene_win/moc_render_modes_node.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp_parameters -/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/python3.12/dist-packages/ost/seq/alg/_ost_seq_alg.so CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.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_alg.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../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 -[ 60%] Linking CXX executable ../../../stage/bin/chemdict_tool -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemdict_tool.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o -o ../../../stage/bin/chemdict_tool -L/build/reproducible-path/openstructure-2.5.0/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_io.so.2.5.0 ../../../stage/lib/libost_mol_alg.so.2.5.0 ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_img_alg.so.2.5.0 ../../../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 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/seq/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/seq/alg/./mat.pyc\",\"mat.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/seq/alg/./renumber.pyc\",\"renumber.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/seq/alg/./aaindex.pyc\",\"aaindex.py\",doraise=True)" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 60%] Built target _ost_seq_alg -make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/depend -make[3]: Entering directory '/build/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/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.dir/DependInfo.cmake "--color=" -[ 60%] Generating scene_win/moc_root_node.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp_parameters -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.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 60%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -[ 60%] Generating scene_win/moc_scene_node.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp_parameters -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -MF CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/wrap_mol_alg.cc -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 60%] Built target chemdict_tool -[ 60%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_svd_superpose.cc -[ 60%] Generating scene_win/moc_scene_win.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp_parameters -[ 60%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -MF CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_symmetry_node.cc -[ 60%] Generating scene_win/moc_scene_win_model.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp_parameters -[ 60%] Linking CXX executable ../../../../stage/bin/lddt -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/lddt.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/lddt.dir/lddt.cc.o -o ../../../../stage/bin/lddt -L/build/reproducible-path/openstructure-2.5.0/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_io.so.2.5.0 ../../../../stage/lib/libost_mol_alg.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5.0 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_conop.so.2.5.0 ../../../../stage/lib/libost_db.so.2.5.0 ../../../../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/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so -[ 60%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/heuristic_block_modifiers.cc -[ 60%] Linking CXX executable ../../stage/bin/molck -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/tools/molck && /usr/bin/cmake -E cmake_link_script CMakeFiles/molck.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/molck.dir/main.cc.o -o ../../stage/bin/molck -L/build/reproducible-path/openstructure-2.5.0/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_io.so.2.5.0 ../../stage/lib/libost_mol_alg.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../stage/lib/libost_seq_alg.so.2.5.0 ../../stage/lib/libost_conop.so.2.5.0 ../../stage/lib/libost_db.so.2.5.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../stage/lib/libost_seq.so.2.5.0 ../../stage/lib/libost_mol.so.2.5.0 ../../stage/lib/libost_img_alg.so.2.5.0 ../../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 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so -[ 60%] Generating sequence_viewer/moc_align_properties_painter.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp_parameters -[ 60%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/interaction.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/interaction.cc.o -MF CMakeFiles/ost_mol_mm.dir/interaction.cc.o.d -o CMakeFiles/ost_mol_mm.dir/interaction.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/interaction.cc -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 60%] Built target lddt -[ 60%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/simulation.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/simulation.cc.o -MF CMakeFiles/ost_mol_mm.dir/simulation.cc.o.d -o CMakeFiles/ost_mol_mm.dir/simulation.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/simulation.cc -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 60%] Built target molck -[ 60%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/modeller.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/modeller.cc.o -MF CMakeFiles/ost_mol_mm.dir/modeller.cc.o.d -o CMakeFiles/ost_mol_mm.dir/modeller.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/modeller.cc -[ 60%] Generating sequence_viewer/moc_alignment_view_object.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp_parameters -[ 62%] Generating sequence_viewer/moc_background_painter.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp_parameters 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, @@ -17098,6 +17000,10 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 58%] Generating scene_win/moc_entity_node.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp_parameters +[ 58%] Generating scene_win/moc_entity_part_node.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp_parameters 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, @@ -17121,64 +17027,49 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 62%] Generating sequence_viewer/moc_base_row.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp_parameters -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/svd_superpose.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_svd_superpose.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_svd_superpose.cc:23: -/usr/include/c++/14/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++/14/bits/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/symmetry_node.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_symmetry_node.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_symmetry_node.cc:19: -/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 58%] Generating scene_win/moc_gfx_scene_node.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_gfx_scene_node.cpp_parameters +[ 58%] Generating scene_win/moc_label_node.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_label_node.cpp_parameters +[ 59%] Generating scene_win/moc_render_mode_node.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp_parameters +[ 59%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/simulation.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/simulation.cc.o -MF CMakeFiles/ost_mol_mm.dir/simulation.cc.o.d -o CMakeFiles/ost_mol_mm.dir/simulation.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/simulation.cc +[ 59%] Generating scene_win/moc_render_modes_node.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp_parameters +[ 59%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/modeller.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/modeller.cc.o -MF CMakeFiles/ost_mol_mm.dir/modeller.cc.o.d -o CMakeFiles/ost_mol_mm.dir/modeller.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/modeller.cc +[ 59%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o -MF CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o.d -o CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/state_extractor.cc +[ 59%] Linking CXX executable ../../../stage/bin/chemdict_tool +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemdict_tool.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o -o ../../../stage/bin/chemdict_tool -L/build/reproducible-path/openstructure-2.5.0/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_io.so.2.5.0 ../../../stage/lib/libost_mol_alg.so.2.5.0 ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_img_alg.so.2.5.0 ../../../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 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so +[ 59%] Generating scene_win/moc_root_node.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp_parameters +[ 59%] Generating scene_win/moc_scene_node.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp_parameters +[ 59%] Generating scene_win/moc_scene_win.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp_parameters +[ 60%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/seq/alg/_ost_seq_alg.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_seq_alg.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/seq/alg/_ost_seq_alg.so CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.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_alg.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../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 +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 60%] Built target chemdict_tool +[ 62%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/observer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/observer.cc.o -MF CMakeFiles/ost_mol_mm.dir/observer.cc.o.d -o CMakeFiles/ost_mol_mm.dir/observer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/observer.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/seq/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/seq/alg/./mat.pyc\",\"mat.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/seq/alg/./renumber.pyc\",\"renumber.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/seq/alg/./aaindex.pyc\",\"aaindex.py\",doraise=True)" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 62%] Built target _ost_seq_alg +[ 62%] Generating scene_win/moc_scene_win_model.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp_parameters +[ 62%] Generating sequence_viewer/moc_align_properties_painter.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp_parameters +[ 62%] Linking CXX executable ../../../../stage/bin/lddt +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/lddt.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/lddt.dir/lddt.cc.o -o ../../../../stage/bin/lddt -L/build/reproducible-path/openstructure-2.5.0/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_io.so.2.5.0 ../../../../stage/lib/libost_mol_alg.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5.0 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_conop.so.2.5.0 ../../../../stage/lib/libost_db.so.2.5.0 ../../../../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/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so 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, @@ -17203,6 +17094,14 @@ /usr/include/c++/14/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' +[ 62%] Built target lddt +[ 62%] Generating sequence_viewer/moc_alignment_view_object.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp_parameters +[ 62%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/system_creator.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/system_creator.cc.o -MF CMakeFiles/ost_mol_mm.dir/system_creator.cc.o.d -o CMakeFiles/ost_mol_mm.dir/system_creator.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/system_creator.cc +[ 63%] Generating sequence_viewer/moc_background_painter.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp_parameters 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/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, @@ -17216,48 +17115,24 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 62%] Generating sequence_viewer/moc_base_view_object.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp_parameters -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/alg/local_dist_diff_test.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/wrap_mol_alg.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/wrap_mol_alg.cc:20: -/usr/include/c++/14/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++/14/bits/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/mol/alg/local_dist_diff_test.hh:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 63%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -MF CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o.d -o CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/topology_creator.cc +[ 63%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/conop/_ost_conop.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_conop.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/conop/_ost_conop.so CMakeFiles/_ost_conop.dir/wrap_conop.cc.o CMakeFiles/_ost_conop.dir/export_compound.cc.o CMakeFiles/_ost_conop.dir/export_processor.cc.o CMakeFiles/_ost_conop.dir/export_heuristic.cc.o CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o CMakeFiles/_ost_conop.dir/export_conop.cc.o CMakeFiles/_ost_conop.dir/export_diag.cc.o CMakeFiles/_ost_conop.dir/export_rule_based.cc.o CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -L/build/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_conop.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../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 +[ 63%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/topology.cc.o -MF CMakeFiles/ost_mol_mm.dir/topology.cc.o.d -o CMakeFiles/ost_mol_mm.dir/topology.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/topology.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, @@ -17278,33 +17153,12 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 62%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_gfx_obj.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/io/mol/pdb_reader.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/simulation.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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 62%] Generating sequence_viewer/moc_conservation_painter.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp_parameters -[ 62%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o -MF CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o.d -o CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/state_extractor.cc -[ 63%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/observer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/observer.cc.o -MF CMakeFiles/ost_mol_mm.dir/observer.cc.o.d -o CMakeFiles/ost_mol_mm.dir/observer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/observer.cc -[ 63%] Generating sequence_viewer/moc_painter.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp_parameters -[ 63%] Generating sequence_viewer/moc_secstr_row.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp_parameters -[ 63%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/system_creator.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/system_creator.cc.o -MF CMakeFiles/ost_mol_mm.dir/system_creator.cc.o.d -o CMakeFiles/ost_mol_mm.dir/system_creator.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/system_creator.cc -[ 63%] Generating sequence_viewer/moc_seq_secstr_painter.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp_parameters +[ 63%] Generating sequence_viewer/moc_base_row.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp_parameters +[ 63%] Linking CXX executable ../../stage/bin/molck +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/tools/molck && /usr/bin/cmake -E cmake_link_script CMakeFiles/molck.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/molck.dir/main.cc.o -o ../../stage/bin/molck -L/build/reproducible-path/openstructure-2.5.0/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_io.so.2.5.0 ../../stage/lib/libost_mol_alg.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../stage/lib/libost_seq_alg.so.2.5.0 ../../stage/lib/libost_conop.so.2.5.0 ../../stage/lib/libost_db.so.2.5.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../stage/lib/libost_seq.so.2.5.0 ../../stage/lib/libost_mol.so.2.5.0 ../../stage/lib/libost_img_alg.so.2.5.0 ../../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 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/conop/./__init__.pyc\",\"__init__.py\",doraise=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, @@ -17334,39 +17188,25 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 64%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_entity.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_entity.cc.o -MF CMakeFiles/_ost_gfx.dir/export_entity.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_entity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_entity.cc -[ 64%] Generating sequence_viewer/moc_seq_selection_painter.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp_parameters -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/gfx_object_base.hh:26, - 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/modules/gfx/pymod/export_gfx_obj.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_gfx_obj.cc:19: -/usr/include/c++/14/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++/14/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/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/conop/./cleanup.pyc\",\"cleanup.py\",doraise=True)" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 63%] Built target _ost_conop +[ 63%] Generating sequence_viewer/moc_base_view_object.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp_parameters +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 63%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/steep.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/steep.cc.o -MF CMakeFiles/ost_mol_mm.dir/steep.cc.o.d -o CMakeFiles/ost_mol_mm.dir/steep.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/steep.cc +[ 63%] Built target molck +make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.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.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 63%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o -MF CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o.d -o CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/wrap_gfx.cc +[ 63%] Generating sequence_viewer/moc_conservation_painter.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp_parameters 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/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, @@ -17377,8 +17217,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 64%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -MF CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o.d -o CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/topology_creator.cc +[ 63%] Generating sequence_viewer/moc_painter.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp_parameters 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, @@ -17402,32 +17242,16 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 64%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_clash.cc -[ 64%] Generating sequence_viewer/moc_seq_text_painter.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp_parameters -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/io/mol/pdb_reader.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35: -/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 64%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/topology.cc.o -MF CMakeFiles/ost_mol_mm.dir/topology.cc.o.d -o CMakeFiles/ost_mol_mm.dir/topology.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/topology.cc -[ 64%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/steep.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_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_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/mm/src/CMakeFiles/ost_mol_mm.dir/steep.cc.o -MF CMakeFiles/ost_mol_mm.dir/steep.cc.o.d -o CMakeFiles/ost_mol_mm.dir/steep.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/steep.cc -[ 64%] Generating sequence_viewer/moc_sequence_delegate.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp_parameters -[ 64%] Generating sequence_viewer/moc_sequence_model.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp_parameters -[ 64%] Generating sequence_viewer/moc_sequence_row.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp_parameters -[ 65%] Generating sequence_viewer/moc_sequence_search_bar.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp_parameters +make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/depend +make[3]: Entering directory '/build/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/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.dir/DependInfo.cmake "--color=" +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.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 63%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -MF CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/wrap_mol_alg.cc +[ 63%] Generating sequence_viewer/moc_secstr_row.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp_parameters 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, @@ -17451,8 +17275,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 65%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_surface.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_surface.cc.o -MF CMakeFiles/_ost_gfx.dir/export_surface.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_surface.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_surface.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, @@ -17476,16 +17298,22 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 65%] Generating sequence_viewer/moc_sequence_table_view.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp_parameters -[ 65%] Generating sequence_viewer/moc_sequence_view_object.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp_parameters -[ 65%] Generating sequence_viewer/moc_sequence_viewer.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp_parameters -[ 65%] Generating sequence_viewer/moc_tick_painter.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp_parameters -[ 65%] Generating sequence_viewer/moc_title_row.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp_parameters +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/io/mol/pdb_reader.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35: +/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 63%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_scene.cc.o -MF CMakeFiles/_ost_gfx.dir/export_scene.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_scene.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_scene.cc +[ 63%] Generating sequence_viewer/moc_seq_secstr_painter.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp_parameters +[ 63%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_svd_superpose.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/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, @@ -17496,13 +17324,20 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 65%] Generating tools/moc_measure_tool.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp_parameters +[ 63%] Generating sequence_viewer/moc_seq_selection_painter.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp_parameters +[ 63%] Generating sequence_viewer/moc_seq_text_painter.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp_parameters +[ 63%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_gfx_node.cc +[ 63%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_clash.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/entity.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_entity.cc:23: + 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/pymod/wrap_gfx.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 | ^~~~~~~~ @@ -17516,7 +17351,7 @@ 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/gfx/pymod/export_entity.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/wrap_gfx.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17526,38 +17361,22 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 65%] Generating tools/moc_tool.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool.cpp_parameters -[ 65%] Generating tools/moc_tool_bar.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_bar.cpp_parameters -[ 67%] Generating tools/moc_tool_manager.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp_parameters -[ 67%] Generating tools/moc_tool_option.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_option.cpp_parameters -[ 67%] Generating tools/moc_tool_option_group.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_option_group.cpp_parameters -[ 67%] Generating tools/moc_tool_options.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options.cpp_parameters -[ 67%] Generating tools/moc_tool_options_widget.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_widget.cpp_parameters -[ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -MF CMakeFiles/_ost_gfx.dir/export_primitives.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_primitives.cc -[ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -MF CMakeFiles/_ost_gfx.dir/export_primlist.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_primlist.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/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.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.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp +[ 63%] Generating sequence_viewer/moc_sequence_delegate.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp_parameters +[ 63%] Generating sequence_viewer/moc_sequence_model.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp_parameters +[ 63%] Generating sequence_viewer/moc_sequence_row.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp_parameters +[ 64%] Generating sequence_viewer/moc_sequence_search_bar.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp_parameters 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/clash_score.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_clash.cc:23: + 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/alg/local_dist_diff_test.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/wrap_mol_alg.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 | ^~~~~~~~ @@ -17571,7 +17390,7 @@ 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/mol/alg/pymod/export_clash.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/wrap_mol_alg.cc:20: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17581,8 +17400,25 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 67%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o +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/mol/alg/local_dist_diff_test.hh: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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 64%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_trajectory_analysis.cc +[ 64%] Generating sequence_viewer/moc_sequence_table_view.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp_parameters +[ 64%] Generating sequence_viewer/moc_sequence_view_object.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp_parameters +[ 64%] Generating sequence_viewer/moc_sequence_viewer.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp_parameters +[ 64%] Generating sequence_viewer/moc_tick_painter.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp_parameters In file included from /usr/include/c++/14/string:54, from /usr/include/c++/14/stdexcept:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, @@ -17669,16 +17505,12 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -[ 67%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_structure_analysis.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/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/surface.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_surface.cc:22: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, + 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/modules/gfx/pymod/export_scene.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 | ^~~~~~~~ @@ -17692,7 +17524,7 @@ 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/gfx/pymod/export_surface.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_scene.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17702,20 +17534,29 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 64%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -MF CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_symmetry_node.cc +[ 64%] Generating sequence_viewer/moc_title_row.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp_parameters 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/gfx_object_base.hh:26, - 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/modules/gui/src/../../../../modules/gui/src/file_browser.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp:10: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_svd_superpose.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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp:9: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_svd_superpose.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17725,13 +17566,32 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 67%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_contact_overlap.cc +[ 64%] Generating tools/moc_measure_tool.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp_parameters +[ 64%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_structure_analysis.cc +[ 64%] Generating tools/moc_tool.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool.cpp_parameters +[ 64%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o +[ 64%] Generating tools/moc_tool_bar.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_gfx_obj.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_bar.cpp_parameters +[ 65%] Generating tools/moc_tool_manager.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp_parameters +[ 65%] Generating tools/moc_tool_option.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_option.cpp_parameters +[ 65%] Generating tools/moc_tool_option_group.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_option_group.cpp_parameters +[ 65%] Generating tools/moc_tool_options.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options.cpp_parameters 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/primitives.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_primitives.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/entity_view.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/clash_score.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_clash.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 | ^~~~~~~~ @@ -17745,7 +17605,7 @@ 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/gfx/pymod/export_primitives.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_clash.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17755,11 +17615,19 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 65%] Generating tools/moc_tool_options_widget.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_widget.cpp_parameters +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.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.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp 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/prim_list.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_primlist.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/trajectory_analysis.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_trajectory_analysis.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 | ^~~~~~~~ @@ -17773,7 +17641,7 @@ 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/gfx/pymod/export_primlist.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_trajectory_analysis.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17783,13 +17651,15 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp +[ 65%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_contact_overlap.cc +[ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_entity.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_entity.cc.o -MF CMakeFiles/_ost_gfx.dir/export_entity.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_entity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_entity.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/alg/trajectory_analysis.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_trajectory_analysis.cc:22: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/symmetry_node.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_symmetry_node.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 | ^~~~~~~~ @@ -17803,7 +17673,32 @@ 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/mol/alg/pymod/export_trajectory_analysis.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_symmetry_node.cc:19: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 67%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_accessibility.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/gfx_object_base.hh:26, + 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/modules/gui/src/../../../../modules/gui/src/file_browser.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp: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 + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/memory:66, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_file_browser.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -17813,10 +17708,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -[ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -MF CMakeFiles/_ost_gfx.dir/export_render_options.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_render_options.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -MF CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_scene_observer.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, @@ -17848,20 +17739,39 @@ /usr/include/c++/14/bits/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/io/seq/sequence_io_handler.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/file_type_dialog.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp:10: -/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{ - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp:9: +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/gfx_object_base.hh:26, + 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/modules/gfx/pymod/export_gfx_obj.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_gfx_obj.cc:19: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp +[ 67%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_sec_structure.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, @@ -17905,38 +17815,8 @@ 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/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/sequence_list.hh: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 - | ^~~~~~~~ -/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_color.cc.o -MF CMakeFiles/_ost_gfx.dir/export_color.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_color.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_color.cc -[ 67%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_accessibility.cc -[ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gradient.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_gradient.cc -[ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -MF CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_color_ops.cc -[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_file_viewer.cpp -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/modules/gfx/pymod/export_color.cc:23: + 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/pymod/export_entity.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 | ^~~~~~~~ @@ -17950,52 +17830,52 @@ 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/gfx/pymod/export_color.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_entity.cc:19: /usr/include/c++/14/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 | ^~~~~~~~ +[ 67%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o +/usr/include/c++/14/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/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_non_standard.cc +[ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_surface.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_surface.cc.o -MF CMakeFiles/_ost_gfx.dir/export_surface.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_surface.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_surface.cc +[ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primitives.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -MF CMakeFiles/_ost_gfx.dir/export_primitives.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_primitives.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/io/seq/sequence_io_handler.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/file_type_dialog.hh:31, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp:10: +/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{ + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/memory:66, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_gl_canvas.cpp -[ 67%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_sec_structure.cc -[ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -MF CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_glwin_base.cc [ 67%] Linking CXX shared library ../../../../stage/lib/libost_mol_mm.so 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/AMBER03.dat /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/forcefields/AMBER03.dat 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/CHARMM27.dat /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/forcefields/CHARMM27.dat cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_mm.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol_mm.so.2.5 -o ../../../../stage/lib/libost_mol_mm.so.2.5.0 CMakeFiles/ost_mol_mm.dir/forcefield.cc.o CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o CMakeFiles/ost_mol_mm.dir/interaction.cc.o CMakeFiles/ost_mol_mm.dir/simulation.cc.o CMakeFiles/ost_mol_mm.dir/modeller.cc.o CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o CMakeFiles/ost_mol_mm.dir/observer.cc.o CMakeFiles/ost_mol_mm.dir/system_creator.cc.o CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o CMakeFiles/ost_mol_mm.dir/topology.cc.o CMakeFiles/ost_mol_mm.dir/steep.cc.o -L/build/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_io.so.2.5.0 /usr/lib/x86_64-linux-gnu/libOpenMM.so ../../../../stage/lib/libost_mol_alg.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 ../../../../stage/lib/libost_conop.so.2.5.0 ../../../../stage/lib/libost_db.so.2.5.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../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 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libtiff.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol_mm.so.2.5.0 ../../../../stage/lib/libost_mol_mm.so.2.5 ../../../../stage/lib/libost_mol_mm.so -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 67%] Built target ost_mol_mm -[ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -MF CMakeFiles/_ost_gfx.dir/export_exporter.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_exporter.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/gradient.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_gradient.cc:29: + 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/sequence_list.hh: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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_gradient.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18005,6 +17885,13 @@ /usr/include/c++/14/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/mm/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol_mm.so.2.5.0 ../../../../stage/lib/libost_mol_mm.so.2.5 ../../../../stage/lib/libost_mol_mm.so +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 67%] Built target ost_mol_mm +[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_file_viewer.cpp +[ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primlist.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -MF CMakeFiles/_ost_gfx.dir/export_primlist.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_primlist.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, @@ -18039,12 +17926,8 @@ 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/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/pymod/export_color_ops.cc:23: + 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/pymod/export_sec_structure.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 | ^~~~~~~~ @@ -18058,7 +17941,7 @@ 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/gfx/pymod/export_color_ops.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_sec_structure.cc:21: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18068,13 +17951,16 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_gl_win.cpp +[ 68%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_molck.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/alg/sec_struct.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_sec_structure.cc:24: + 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/obj-x86_64-linux-gnu/stage/include/ost/mol/surface.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/surface.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_surface.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 | ^~~~~~~~ @@ -18088,7 +17974,7 @@ 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/mol/alg/pymod/export_sec_structure.cc:21: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_surface.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18098,20 +17984,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 67%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_non_standard.cc -[ 68%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -MF CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_bitmap.cc -[ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o -MF CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_menu.cpp -[ 68%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_map.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_map.cc.o -MF CMakeFiles/_ost_gfx.dir/export_map.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_map.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_map.cc -[ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_gosty_app.cpp -[ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_main.cpp -[ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main_area.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_main_area.cpp +[ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_gl_canvas.cpp 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, @@ -18143,19 +18017,13 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -MF CMakeFiles/ost_gui.dir/moc_perspective.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_perspective.cpp -[ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -MF CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_dock_widget.cpp +[ 68%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_membrane.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/image.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_iso.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_map.cc:23: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/primitives.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_primitives.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 | ^~~~~~~~ @@ -18169,7 +18037,7 @@ 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/gfx/pymod/export_map.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_primitives.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18179,34 +18047,27 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 70%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_molck.cc -[ 70%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_membrane.cc -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main_window.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_main_window.cpp -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -MF CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_widget.cpp -[ 70%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o +[ 68%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/export_entity_to_density.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/query_view_wrapper.hh:24, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/scene_selection.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp:10: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/prim_list.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_primlist.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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp:9: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_primlist.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18216,28 +18077,12 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_geom_handler.cpp -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_pool.cpp -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_main.cpp:10: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh: In instantiation of 'ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]': -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:40:25: required from here - 40 | class DLLEXPORT_OST_GUI GostyMainWindow : public WidgetStateSaver - | ^~~~~~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh:323:8: warning: the address of 'ost::gui::WidgetStateSaver::QMainWindow' will never be NULL [-Waddress] - 323 | if(dynamic_cast(this)){ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::QMainWindow' declared here - 263 | class WidgetStateSaver: public BASE - | ^~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_message_widget.cpp -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_message_box_widget.cpp -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_log_reader.cpp +[ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_gl_win.cpp +[ 68%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -MF CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_scene_observer.cc +[ 68%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_render_options.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -MF CMakeFiles/_ost_gfx.dir/export_render_options.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_render_options.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, @@ -18262,8 +18107,12 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp +[ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o -MF CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_menu.cpp +[ 68%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_color.cc.o -MF CMakeFiles/_ost_gfx.dir/export_color.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_color.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_color.cc +[ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_gosty_app.cpp 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, @@ -18296,16 +18145,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp -[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp -[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp -[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp -[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp 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, @@ -18337,6 +18176,181 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 68%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gradient.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gradient.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_gradient.cc +[ 68%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -MF CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_color_ops.cc +[ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_main.cpp +[ 68%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -MF CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_glwin_base.cc +[ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_area.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main_area.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_main_area.cpp +[ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_perspective.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -MF CMakeFiles/ost_gui.dir/moc_perspective.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_perspective.cpp +[ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -MF CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_dock_widget.cpp +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/gradient.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_gradient.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_gradient.cc:24: +/usr/include/c++/14/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++/14/bits/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/modules/gfx/pymod/export_color.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_color.cc:19: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_window.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main_window.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_main_window.cpp +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/pymod/export_color_ops.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_color_ops.cc:19: +/usr/include/c++/14/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++/14/bits/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/modules/gui/src/../../../../modules/gui/src/main.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_main.cpp:10: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh: In instantiation of 'ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]': +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:40:25: required from here + 40 | class DLLEXPORT_OST_GUI GostyMainWindow : public WidgetStateSaver + | ^~~~~~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh:323:8: warning: the address of 'ost::gui::WidgetStateSaver::QMainWindow' will never be NULL [-Waddress] + 323 | if(dynamic_cast(this)){ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::QMainWindow' declared here + 263 | class WidgetStateSaver: public BASE + | ^~~~~~~~~~~~~~~~~~~~~~ +[ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -MF CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp +[ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_widget.cpp +[ 69%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_exporter.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -MF CMakeFiles/_ost_gfx.dir/export_exporter.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_exporter.cc +[ 70%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -MF CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_bitmap.cc +[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_geom_handler.cpp +[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_widget_pool.cpp +[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_message_widget.cpp +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/modules/gui/src/../../../../modules/gui/src/scene_selection.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp: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 + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/memory:66, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/moc_scene_selection.cpp:9: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_message_box_widget.cpp +[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/messages/moc_log_reader.cpp +[ 70%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_map.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -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/pymod/CMakeFiles/_ost_gfx.dir/export_map.cc.o -MF CMakeFiles/_ost_gfx.dir/export_map.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_map.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_map.cc +[ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp +[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp +[ 72%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/mol/alg/_ost_mol_alg.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol_alg.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/mol/alg/_ost_mol_alg.so CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -L/build/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_mol_alg.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5.0 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_conop.so.2.5.0 ../../../../stage/lib/libost_db.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../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 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../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/libsqlite3.so +[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp +[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp +[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp 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, @@ -18363,8 +18377,12 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp +[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./views.pyc\",\"views.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./superpose.pyc\",\"superpose.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./qsscoring.pyc\",\"qsscoring.py\",doraise=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, @@ -18391,8 +18409,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp 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, @@ -18401,15 +18417,15 @@ 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/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp:10: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/conservation_painter.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18419,19 +18435,33 @@ /usr/include/c++/14/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/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./trajectory_analysis.pyc\",\"trajectory_analysis.py\",doraise=True)" +trajectory_analysis.py:59: SyntaxWarning: invalid escape sequence '\ ' +trajectory_analysis.py:98: SyntaxWarning: invalid escape sequence '\ ' +trajectory_analysis.py:141: SyntaxWarning: invalid escape sequence '\ ' +trajectory_analysis.py:174: SyntaxWarning: invalid escape sequence '\ ' +trajectory_analysis.py:233: SyntaxWarning: invalid escape sequence '\ ' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./structure_analysis.pyc\",\"structure_analysis.py\",doraise=True)" +structure_analysis.py:65: SyntaxWarning: invalid escape sequence '\ ' +structure_analysis.py:157: SyntaxWarning: invalid escape sequence '\ ' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./helix_kinks.pyc\",\"helix_kinks.py\",doraise=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/chain_view.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/secstr_row.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:10: + 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/alg/sec_structure_segments.hh:25, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18441,6 +18471,10 @@ /usr/include/c++/14/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/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./hbond.pyc\",\"hbond.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./lddt.pyc\",\"lddt.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./qsscore.pyc\",\"qsscore.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./scoring.pyc\",\"scoring.py\",doraise=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, @@ -18466,23 +18500,39 @@ /usr/include/c++/14/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/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./chain_mapping.pyc\",\"chain_mapping.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./stereochemistry.pyc\",\"stereochemistry.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./ligand_scoring.pyc\",\"ligand_scoring.py\",doraise=True)" +[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./dockq.pyc\",\"dockq.py\",doraise=True)" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 72%] Built target _ost_mol_alg +make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/depend +make[3]: Entering directory '/build/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.dir/DependInfo.cmake "--color=" +[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/build +[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 72%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/wrap_io.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/wrap_io.cc.o -MF CMakeFiles/_ost_io.dir/wrap_io.cc.o.d -o CMakeFiles/_ost_io.dir/wrap_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/wrap_io.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/alg/sec_structure_segments.hh:25, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/conservation_painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:10: + 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/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/secstr_row.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18492,6 +18542,12 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp +[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp +[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp 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, @@ -18518,10 +18574,42 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp -[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp +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/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_iso.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_map.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/export_map.cc:19: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 73%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_pdb_io.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_pdb_io.cc.o -MF CMakeFiles/_ost_io.dir/export_pdb_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_pdb_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_pdb_io.cc +[ 73%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o -MF CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_mmcif_io.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, @@ -18548,10 +18636,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp -[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp 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, @@ -18580,12 +18664,6 @@ | ^~~~~~~~ [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp -[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp -[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp -[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp 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, @@ -18609,55 +18687,19 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp -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/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: -/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 73%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/mol/alg/_ost_mol_alg.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol_alg.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/mol/alg/_ost_mol_alg.so CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -L/build/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_mol_alg.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5.0 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_conop.so.2.5.0 ../../../../stage/lib/libost_db.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../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 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../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/libsqlite3.so -[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" -[ 73%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/gfx/_ost_gfx.so -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/gradients.xml /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/scene/gradients.xml -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./views.pyc\",\"views.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_gfx.dir/link.txt --verbose=1 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./superpose.pyc\",\"superpose.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 -o ../../../stage/lib/python3.12/dist-packages/ost/gfx/_ost_gfx.so CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o CMakeFiles/_ost_gfx.dir/export_scene.cc.o CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o CMakeFiles/_ost_gfx.dir/export_entity.cc.o CMakeFiles/_ost_gfx.dir/export_surface.cc.o CMakeFiles/_ost_gfx.dir/export_primitives.cc.o CMakeFiles/_ost_gfx.dir/export_primlist.cc.o CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o CMakeFiles/_ost_gfx.dir/export_render_options.cc.o CMakeFiles/_ost_gfx.dir/export_color.cc.o CMakeFiles/_ost_gfx.dir/export_gradient.cc.o CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o CMakeFiles/_ost_gfx.dir/export_exporter.cc.o CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o CMakeFiles/_ost_gfx.dir/export_map.cc.o -L/build/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_gfx.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../stage/lib/libost_img_alg.so.2.5.0 ../../../stage/lib/libost_img.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 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./qsscoring.pyc\",\"qsscoring.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./trajectory_analysis.pyc\",\"trajectory_analysis.py\",doraise=True)" -trajectory_analysis.py:59: SyntaxWarning: invalid escape sequence '\ ' -trajectory_analysis.py:98: SyntaxWarning: invalid escape sequence '\ ' -trajectory_analysis.py:141: SyntaxWarning: invalid escape sequence '\ ' -trajectory_analysis.py:174: SyntaxWarning: invalid escape sequence '\ ' -trajectory_analysis.py:233: SyntaxWarning: invalid escape sequence '\ ' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./structure_analysis.pyc\",\"structure_analysis.py\",doraise=True)" -structure_analysis.py:65: SyntaxWarning: invalid escape sequence '\ ' -structure_analysis.py:157: SyntaxWarning: invalid escape sequence '\ ' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./helix_kinks.pyc\",\"helix_kinks.py\",doraise=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/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/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_row.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:10: + 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/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18667,21 +18709,38 @@ /usr/include/c++/14/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/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./hbond.pyc\",\"hbond.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./lddt.pyc\",\"lddt.py\",doraise=True)" +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/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: +/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++/14/bits/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/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: +/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++/14/bits/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/chain_view.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:10: + 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/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_row.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18691,7 +18750,12 @@ /usr/include/c++/14/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/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./qsscore.pyc\",\"qsscore.py\",doraise=True)" +[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp +[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp +[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp 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, @@ -18718,7 +18782,6 @@ /usr/include/c++/14/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/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./scoring.pyc\",\"scoring.py\",doraise=True)" 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] @@ -18727,25 +18790,30 @@ /usr/include/c++/14/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/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./chain_mapping.pyc\",\"chain_mapping.py\",doraise=True)" +[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp 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/alg/sec_structure_segments.hh:25, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/title_row.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:10: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_pdb_io.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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:9: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_pdb_io.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18755,23 +18823,34 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 73%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_omf_io.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_omf_io.cc.o -MF CMakeFiles/_ost_io.dir/export_omf_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_omf_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_omf_io.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/io/mol/pdb_reader.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_pdb_io.cc:23: +/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 74%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_map_io.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_map_io.cc.o -MF CMakeFiles/_ost_io.dir/export_map_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_map_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_map_io.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/alg/sec_structure_segments.hh:25, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/tick_painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:10: + 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/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_table_view.hh:29, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18781,35 +18860,28 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp -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/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: -/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++/14/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/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./stereochemistry.pyc\",\"stereochemistry.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./ligand_scoring.pyc\",\"ligand_scoring.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/mol/alg/./dockq.pyc\",\"dockq.py\",doraise=True)" -make[3]: Leaving 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/mol/chain_view.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_table_view.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:10: + 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/io/mol/io_profile.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_mmcif_io.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++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:9: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_mmcif_io.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18819,34 +18891,23 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 73%] Built target _ost_mol_alg -make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/depend -make[3]: Entering directory '/build/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.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 73%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/wrap_io.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/wrap_io.cc.o -MF CMakeFiles/_ost_io.dir/wrap_io.cc.o.d -o CMakeFiles/_ost_io.dir/wrap_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/wrap_io.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/gfx/./__init__.pyc\",\"__init__.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/gfx/./py_gfx_obj.pyc\",\"py_gfx_obj.py\",doraise=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/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/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_viewer.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp:10: + 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/alg/sec_structure_segments.hh:25, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/tick_painter.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18856,12 +18917,9 @@ /usr/include/c++/14/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' -[ 73%] Built target _ost_gfx -[ 73%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_pdb_io.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_pdb_io.cc.o -MF CMakeFiles/_ost_io.dir/export_pdb_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_pdb_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_pdb_io.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/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_mmcif_io.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{ | ^~~~~~~~ @@ -18869,10 +18927,23 @@ 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/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/wrap_io.cc:23: /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{ | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/wrap_io.cc:20: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18884,15 +18955,35 @@ 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/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/alignment_view_object.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:10: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_viewer.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp:9: +/usr/include/c++/14/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++/14/bits/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/sequence_list.hh: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 + | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18903,6 +18994,14 @@ 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/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: +/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++/14/bits/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{ @@ -18910,8 +19009,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp +[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp 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, @@ -18921,15 +19020,15 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_view_object.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:10: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/title_row.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18939,35 +19038,27 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_main_thread_runner.cpp -[ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp -[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG 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CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp +[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp +[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp 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/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:10: + 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/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/alignment_view_object.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -18977,46 +19068,33 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter_worker.cpp -[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_namespace_tree_model.cpp -In file included from /build/reproducible-path/openstructure-2.5.0/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, - 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/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:30: -/build/reproducible-path/openstructure-2.5.0/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); - | ^~~~~~~~ -[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell.cpp 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/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:32: + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp -[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp -[ 74%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o -MF CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_mmcif_io.cc -[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_state_machine.cpp -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/io/seq/sequence_io_handler.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/io_manager.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/wrap_io.cc:23: -/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{ - | ^~~~~~~~ +[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_main_thread_runner.cpp +[ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_gutter.cpp +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/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_map_io.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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, @@ -19027,21 +19105,7 @@ 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/io/pymod/wrap_io.cc:20: -/usr/include/c++/14/bits/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/sequence_list.hh: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 - | ^~~~~~~~ + from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_map_io.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19057,8 +19121,8 @@ 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/io/mol/io_profile.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_pdb_io.cc:22: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_omf_io.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 | ^~~~~~~~ @@ -19072,7 +19136,7 @@ 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/io/pymod/export_pdb_io.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_omf_io.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19082,45 +19146,33 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_state.cpp 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/io/mol/pdb_reader.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_pdb_io.cc:23: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mmcif_info.hh:25, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_transition.cpp -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_transition_guard.cpp -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_bar.cpp -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_bar.cpp -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_manager.cpp -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_bottom_bar.cpp 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/gfx_object_base.hh:26, - 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/modules/gui/src/panels/../../../../../modules/gui/src/panels/drop_box.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp:10: + 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/alg/sec_structure_segments.hh:25, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_view_object.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19130,32 +19182,23 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_box.cpp -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_event_button.cpp +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_output_redirector.cpp 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/io/mol/io_profile.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_mmcif_io.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp: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 | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_mmcif_io.cc:19: +In file included from /usr/include/c++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/memory:66, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19165,58 +19208,133 @@ /usr/include/c++/14/bits/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/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, + 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/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:30: +/build/reproducible-path/openstructure-2.5.0/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/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/io/mol/mmcif_reader.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_mmcif_io.cc:27: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:32: /build/reproducible-path/openstructure-2.5.0/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_path_completer.cpp +[ 75%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/gfx/_ost_gfx.so +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/gradients.xml /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/scene/gradients.xml +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_gfx.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/gfx/_ost_gfx.so CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o CMakeFiles/_ost_gfx.dir/export_scene.cc.o CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o CMakeFiles/_ost_gfx.dir/export_entity.cc.o CMakeFiles/_ost_gfx.dir/export_surface.cc.o CMakeFiles/_ost_gfx.dir/export_primitives.cc.o CMakeFiles/_ost_gfx.dir/export_primlist.cc.o CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o CMakeFiles/_ost_gfx.dir/export_render_options.cc.o CMakeFiles/_ost_gfx.dir/export_color.cc.o CMakeFiles/_ost_gfx.dir/export_gradient.cc.o CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o CMakeFiles/_ost_gfx.dir/export_exporter.cc.o CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o CMakeFiles/_ost_gfx.dir/export_map.cc.o -L/build/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_gfx.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../stage/lib/libost_img_alg.so.2.5.0 ../../../stage/lib/libost_img.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 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so /usr/lib/x86_64-linux-gnu/libOpenGL.so /usr/lib/x86_64-linux-gnu/libGLX.so /usr/lib/x86_64-linux-gnu/libGLU.so /usr/lib/x86_64-linux-gnu/libpng.so /usr/lib/x86_64-linux-gnu/libz.so +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_completer.cpp +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter_worker.cpp +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_namespace_tree_model.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/gfx/./__init__.pyc\",\"__init__.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/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/python3.12/dist-packages//ost/gfx/./py_gfx_obj.pyc\",\"py_gfx_obj.py\",doraise=True)" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 75%] Built target _ost_gfx +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell.cpp +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp +[ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB 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-MF CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/python_shell/moc_state.cpp +[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o -c 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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/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_bar.cpp +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK 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-D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp +[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI 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/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_bar.cpp +[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_manager.cpp +[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_bottom_bar.cpp +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/gfx_object_base.hh:26, + 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/modules/gui/src/panels/../../../../../modules/gui/src/panels/drop_box.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp: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 + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/memory:66, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp:9: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_button_box.cpp +[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_event_button.cpp +[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_widget_container.cpp -[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o +[ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_panel_bar_widget_holder.cpp -[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o +[ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_side_bar.cpp -[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o +[ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_splitter_panel_bar.cpp -[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o +[ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/panels/moc_tabbed_panel_bar.cpp -[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o +[ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB 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modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp -[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o +[ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o -MF 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-DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp -[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o +[ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_gfx_scene_node.cpp -[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o +[ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_label_node.cpp -[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o +[ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp -[ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o +[ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp -[ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp 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/gui/scene_win/scene_win_model.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/context_menu.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:10: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/current_selection_node.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19232,15 +19350,17 @@ 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/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/current_selection_node.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:10: + 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/gui/scene_win/scene_win_model.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/context_menu.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19250,12 +19370,18 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp -[ 78%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_omf_io.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_omf_io.cc.o -MF CMakeFiles/_ost_io.dir/export_omf_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_omf_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_omf_io.cc -[ 79%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_map_io.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_map_io.cc.o -MF CMakeFiles/_ost_io.dir/export_map_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_map_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_map_io.cc +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp 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, @@ -19281,23 +19407,21 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp -[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp 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/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_node.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:10: + 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/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19307,6 +19431,10 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool.cpp +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_option_group.cpp 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, @@ -19332,25 +19460,21 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp -[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp +[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options.cpp 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/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:10: + 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/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_node.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19360,32 +19484,22 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool.cpp -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: -/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/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_modes_node.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp:10: + 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/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/scene_win.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19395,16 +19509,10 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_option_group.cpp -[ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options.cpp [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_bar.cpp [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_option.cpp -[ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp 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, @@ -19430,24 +19538,32 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_widget.cpp +[ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp +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: +/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/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/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/scene_win.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp:10: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_modes_node.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19457,41 +19573,10 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_widget.cpp [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp -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/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_map_io.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_map_io.cc:19: -/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_argand.cpp.o @@ -19500,50 +19585,16 @@ cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp -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/io/mol/omf.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_omf_io.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/export_omf_io.cc:19: -/usr/include/c++/14/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++/14/bits/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/io/mmcif_info.hh:25, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_manager_gui.cpp +[ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp +[ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_null_overlay.cpp +[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_base.cpp 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, @@ -19568,10 +19619,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -[ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_null_overlay.cpp 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, @@ -19601,18 +19648,16 @@ 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/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/image_handle.hh:38, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data_observer.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/fft_panel.hh:30, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp:10: + 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/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19622,21 +19667,21 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -c /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_base.cpp 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/modules/gui/src/tools/../../../../../modules/gui/src/tools/measure_tool.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp:10: + 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/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19651,18 +19696,16 @@ 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/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp:10: + 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/modules/gui/src/tools/../../../../../modules/gui/src/tools/measure_tool.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19677,16 +19720,18 @@ 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/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:10: + 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/image_handle.hh:38, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data_observer.hh:31, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/fft_panel.hh:30, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp: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 | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:9: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp:9: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19699,11 +19744,19 @@ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/thin_splitter.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/thin_splitter.cc.o -MF CMakeFiles/ost_gui.dir/thin_splitter.cc.o.d -o CMakeFiles/ost_gui.dir/thin_splitter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/thin_splitter.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/perspective.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/perspective.cc.o -MF CMakeFiles/ost_gui.dir/perspective.cc.o.d -o CMakeFiles/ost_gui.dir/perspective.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/perspective.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_registry.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_registry.cc.o -MF CMakeFiles/ost_gui.dir/widget_registry.cc.o.d -o CMakeFiles/ost_gui.dir/widget_registry.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/widget_registry.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/perspective.cc.o -MF CMakeFiles/ost_gui.dir/perspective.cc.o.d -o CMakeFiles/ost_gui.dir/perspective.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/perspective.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_browser.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_browser.cc.o -MF CMakeFiles/ost_gui.dir/file_browser.cc.o.d -o CMakeFiles/ost_gui.dir/file_browser.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_browser.cc +[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -MF CMakeFiles/ost_gui.dir/file_type_dialog.cc.o.d -o CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_type_dialog.cc +[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_viewer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_viewer.cc.o -MF CMakeFiles/ost_gui.dir/file_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/file_viewer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_viewer.cc +[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main.cc.o -MF CMakeFiles/ost_gui.dir/main.cc.o.d -o CMakeFiles/ost_gui.dir/main.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/main.cc +[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_canvas.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gl_canvas.cc.o -MF CMakeFiles/ost_gui.dir/gl_canvas.cc.o.d -o CMakeFiles/ost_gui.dir/gl_canvas.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/gl_canvas.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, @@ -19727,22 +19780,10 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -MF CMakeFiles/ost_gui.dir/file_type_dialog.cc.o.d -o CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_type_dialog.cc -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_viewer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_viewer.cc.o -MF CMakeFiles/ost_gui.dir/file_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/file_viewer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_viewer.cc -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main.cc.o -MF CMakeFiles/ost_gui.dir/main.cc.o.d -o CMakeFiles/ost_gui.dir/main.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/main.cc -[ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_canvas.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gl_canvas.cc.o -MF CMakeFiles/ost_gui.dir/gl_canvas.cc.o.d -o CMakeFiles/ost_gui.dir/gl_canvas.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/gl_canvas.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/dock_widget.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/dock_widget.cc.o -MF CMakeFiles/ost_gui.dir/dock_widget.cc.o.d -o CMakeFiles/ost_gui.dir/dock_widget.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/dock_widget.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main_window.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main_window.cc.o -MF CMakeFiles/ost_gui.dir/main_window.cc.o.d -o CMakeFiles/ost_gui.dir/main_window.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/main_window.cc -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o -MF CMakeFiles/ost_gui.dir/gl_win.cc.o.d -o CMakeFiles/ost_gui.dir/gl_win.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/gl_win.cc -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o -MF CMakeFiles/ost_gui.dir/scene_menu.cc.o.d -o CMakeFiles/ost_gui.dir/scene_menu.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_menu.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/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_type_dialog.hh:31, @@ -19759,32 +19800,10 @@ /usr/include/c++/14/bits/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/gfx_object_base.hh:26, - 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/gui/file_browser.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/perspective.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/platform.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/perspective.cc:20: -/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o -MF CMakeFiles/ost_gui.dir/gl_win.cc.o.d -o CMakeFiles/ost_gui.dir/gl_win.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/gl_win.cc +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o -MF CMakeFiles/ost_gui.dir/scene_menu.cc.o.d -o CMakeFiles/ost_gui.dir/scene_menu.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_menu.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, @@ -19811,39 +19830,23 @@ cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/admin.cc.o -MF CMakeFiles/ost_gui.dir/admin.cc.o.d -o CMakeFiles/ost_gui.dir/admin.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/admin.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_pool.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_pool.cc.o -MF CMakeFiles/ost_gui.dir/widget_pool.cc.o.d -o CMakeFiles/ost_gui.dir/widget_pool.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/widget_pool.cc -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -MF CMakeFiles/ost_gui.dir/messages/message_widget.cc.o.d -o CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/messages/message_widget.cc -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -MF CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o.d -o CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/messages/message_box_widget.cc -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/log_reader.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/log_reader.cc.o -MF CMakeFiles/ost_gui.dir/messages/log_reader.cc.o.d -o CMakeFiles/ost_gui.dir/messages/log_reader.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/messages/log_reader.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/gui/src/file_browser.cc:23: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, + 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/gui/file_browser.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/perspective.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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - from /usr/include/c++/14/math.h:36, - from /usr/include/python3.12/pyport.h:195, - from /usr/include/python3.12/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_browser.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/obj-x86_64-linux-gnu/stage/include/ost/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/platform.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/perspective.cc:20: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19853,16 +19856,18 @@ /usr/include/c++/14/bits/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/io/seq/sequence_io_handler.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_browser.cc:34: -/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -MF CMakeFiles/ost_gui.dir/messages/message_widget.cc.o.d -o CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/messages/message_widget.cc +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -MF CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o.d -o CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/messages/message_box_widget.cc +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/log_reader.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/log_reader.cc.o -MF CMakeFiles/ost_gui.dir/messages/log_reader.cc.o.d -o CMakeFiles/ost_gui.dir/messages/log_reader.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/messages/log_reader.cc +[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/align_properties_painter.cc +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_row.cc +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/background_painter.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, @@ -19889,22 +19894,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(QWidget*)': -/build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_browser.cc:62:13: warning: 'QDirModel::QDirModel(QObject*)' is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] - 62 | model_(new QDirModel), - | ^~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDirModel:1, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_browser.cc:53: -/usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here - 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); - | ^~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(const QString&, QWidget*)': -/build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_browser.cc:102:13: warning: 'QDirModel::QDirModel(QObject*)' is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] - 102 | model_(new QDirModel), - | ^~~~~~~~~ -/usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here - 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); - | ^~~~~~~~~ In file included from /build/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, @@ -19940,25 +19929,14 @@ /usr/include/c++/14/bits/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/io/seq/sequence_io_handler.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:30: -/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/align_properties_painter.cc -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_row.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/gui/src/gl_win.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/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/gui/src/file_browser.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 | ^~~~~~~~ @@ -19977,7 +19955,7 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/gl_win.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_browser.cc:20: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -19987,6 +19965,27 @@ /usr/include/c++/14/bits/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/io/seq/sequence_io_handler.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:30: +/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/conservation_painter.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/io/seq/sequence_io_handler.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/file_loader.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_browser.cc:34: +/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++/14/bits/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/gui/main.hh:28: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh: In instantiation of 'ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]': /build/reproducible-path/openstructure-2.5.0/modules/gui/src/main.cc:70:69: required from here @@ -20017,8 +20016,50 @@ 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/gui/src/scene_menu.cc:21: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/painter.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_row.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_row.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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3898, + 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: +/usr/include/c++/14/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(QWidget*)': +/build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_browser.cc:62:13: warning: 'QDirModel::QDirModel(QObject*)' is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] + 62 | model_(new QDirModel), + | ^~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDirModel:1, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_browser.cc:53: +/usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here + 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); + | ^~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(const QString&, QWidget*)': +/build/reproducible-path/openstructure-2.5.0/modules/gui/src/file_browser.cc:102:13: warning: 'QDirModel::QDirModel(QObject*)' is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] + 102 | model_(new QDirModel), + | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here + 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); + | ^~~~~~~~~ +In file included from /build/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/gui/src/gl_win.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 | ^~~~~~~~ @@ -20037,7 +20078,7 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_menu.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/gl_win.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -20047,18 +20088,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/background_painter.cc -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/conservation_painter.cc -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/secstr_row.cc -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_secstr_painter.cc -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_selection_painter.cc -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_text_painter.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, @@ -20067,8 +20096,8 @@ 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/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/align_properties_painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/align_properties_painter.cc:26: + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/background_painter.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/background_painter.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 | ^~~~~~~~ @@ -20087,6 +20116,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/secstr_row.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, @@ -20095,8 +20126,8 @@ 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/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_row.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_row.cc:26: + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/align_properties_painter.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/align_properties_painter.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 | ^~~~~~~~ @@ -20121,19 +20152,27 @@ 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/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/alg/sec_structure_segments.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/background_painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/background_painter.cc: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/gui/src/scene_menu.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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, - 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: + from /usr/include/c++/14/math.h:36, + from /usr/include/python3.12/pyport.h:195, + from /usr/include/python3.12/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/main.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_menu.cc:19: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -20143,8 +20182,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_delegate.cc +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_secstr_painter.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, @@ -20173,8 +20212,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_model.cc +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_selection_painter.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, @@ -20183,8 +20222,8 @@ 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/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_selection_painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_selection_painter.cc:26: + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_secstr_painter.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_secstr_painter.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 | ^~~~~~~~ @@ -20203,16 +20242,22 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_text_painter.cc +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_delegate.cc +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_model.cc +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_row.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/alg/sec_structure_segments.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_secstr_painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_secstr_painter.cc: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/gui/src/sequence_viewer/secstr_row.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 | ^~~~~~~~ @@ -20231,14 +20276,31 @@ /usr/include/c++/14/bits/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/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, + 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/gui/src/sequence_viewer/secstr_row.cc:29: +/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); + | ^~~~~~~~ +[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_search_bar.cc +[ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_table_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/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/gui/src/sequence_viewer/secstr_row.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/painter.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_selection_painter.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_selection_painter.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 | ^~~~~~~~ @@ -20257,6 +20319,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_viewer.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, @@ -20265,8 +20329,9 @@ 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/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_text_painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_text_painter.cc:26: + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_row.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/title_row.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_model.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 | ^~~~~~~~ @@ -20285,26 +20350,16 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_row.cc -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, - 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/gui/src/sequence_viewer/secstr_row.cc:29: -/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/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/gui/src/sequence_viewer/sequence_model.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_delegate.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_delegate.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/alg/sec_structure_segments.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/painter.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_text_painter.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_text_painter.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 | ^~~~~~~~ @@ -20313,7 +20368,7 @@ from /usr/include/c++/14/cmath:3898, 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/chain_view.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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -20323,27 +20378,13 @@ /usr/include/c++/14/bits/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/gui/src/sequence_viewer/sequence_model.hh:30: -/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_search_bar.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/alg/sec_structure_segments.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_row.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/title_row.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_model.cc:25: + 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/gui/src/sequence_viewer/sequence_model.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_delegate.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_delegate.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 | ^~~~~~~~ @@ -20352,7 +20393,7 @@ from /usr/include/c++/14/cmath:3898, 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: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:22: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -20362,20 +20403,16 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_table_view.cc -[ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_viewer.cc -[ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/tick_painter.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/gui/src/sequence_viewer/sequence_row.cc:26: + 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/gui/src/sequence_viewer/sequence_search_bar.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_search_bar.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 | ^~~~~~~~ @@ -20383,8 +20420,8 @@ from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, 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: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/module_config.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_search_bar.hh:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -20395,30 +20432,26 @@ 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/gui/src/sequence_viewer/sequence_model.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_model.cc:30: + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -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, - 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/gui/src/sequence_viewer/sequence_row.cc:29: -/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); - | ^~~~~~~~ -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/title_row.cc -/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/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_view_object.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_row.cc:31: + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_model.hh:30: +/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/tick_painter.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/modules/gui/src/sequence_viewer/sequence_model.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_model.cc:30: /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{ | ^~~~~~~~ @@ -20436,18 +20469,14 @@ /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); | ^~~~~~~~ -[ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/alignment_view_object.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_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/gui/src/sequence_viewer/sequence_search_bar.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_search_bar.cc:23: + 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/gui/src/sequence_viewer/sequence_row.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 | ^~~~~~~~ @@ -20455,8 +20484,8 @@ from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, 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/gui/module_config.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_search_bar.hh:25: + 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -20466,16 +20495,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_view_object.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++/14/bits/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, @@ -20502,6 +20521,28 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/title_row.cc +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, + 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/gui/src/sequence_viewer/sequence_row.cc:29: +/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/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_view_object.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_row.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++/14/bits/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/gui/src/sequence_viewer/sequence_model.hh:30: /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] @@ -20510,6 +20551,10 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/alignment_view_object.cc +[ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_view_object.cc [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_view_object.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, @@ -20536,35 +20581,6 @@ /usr/include/c++/14/bits/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/mol/alg/sec_structure_segments.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/painter.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_row.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_view_object.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_view_object.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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3898, - 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: -/usr/include/c++/14/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++/14/bits/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/gui/src/sequence_viewer/sequence_model.hh:30: /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] @@ -20573,18 +20589,23 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gosty_app.cc.o [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main_area.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gosty_app.cc.o -MF CMakeFiles/ost_gui.dir/gosty_app.cc.o.d -o CMakeFiles/ost_gui.dir/gosty_app.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/gosty_app.cc +[ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gosty_app.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main_area.cc.o -MF CMakeFiles/ost_gui.dir/main_area.cc.o.d -o CMakeFiles/ost_gui.dir/main_area.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/main_area.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gosty_app.cc.o -MF CMakeFiles/ost_gui.dir/gosty_app.cc.o.d -o CMakeFiles/ost_gui.dir/gosty_app.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/gosty_app.cc +[ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_state_saver.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_state_saver.cc.o -MF CMakeFiles/ost_gui.dir/widget_state_saver.cc.o.d -o CMakeFiles/ost_gui.dir/widget_state_saver.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gui/src/widget_state_saver.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/gui/src/sequence_viewer/alignment_view_object.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/painter.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_row.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_view_object.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_view_object.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 | ^~~~~~~~ @@ -20603,23 +20624,6 @@ /usr/include/c++/14/bits/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/aligned_region.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/alignment_view_object.cc: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++/14/bits/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