Diff of the two buildlogs: -- --- b1/build.log 2025-04-02 02:50:43.786994197 +0000 +++ b2/build.log 2025-04-02 03:04:47.675891698 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 1 14:01:48 -12 2025 -I: pbuilder-time-stamp: 1743559308 +I: Current time: Tue May 5 23:14:03 +14 2026 +I: pbuilder-time-stamp: 1777972443 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: applying promod-executable.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/899332/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1156461/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 5 09:14 /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/1156461/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1156461/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='6a35ccae22424094aeb13524a2e22d36' - 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='899332' - PS1='# ' - PS2='> ' + INVOCATION_ID=9f14fae2441041a9b601e5693d0fa2af + 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=1156461 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.pBMlAM1B/pbuilderrc_U26K --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.pBMlAM1B/b1 --logfile b1/build.log promod3_3.4.2+ds-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.pBMlAM1B/pbuilderrc_R8cM --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.pBMlAM1B/b2 --logfile b2/build.log promod3_3.4.2+ds-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/899332/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1156461/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -453,7 +485,7 @@ Get: 298 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5 amd64 5.15.11+dfsg-2 [2508 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 python3-ost amd64 2.9.3-1 [3992 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 openstructure amd64 2.9.3-1 [93.1 MB] -Fetched 339 MB in 12s (28.1 MB/s) +Fetched 339 MB in 7s (47.6 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-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 ... 19804 files and directories currently installed.) @@ -1433,8 +1465,8 @@ Setting up tzdata (2025b-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Apr 2 02:07:36 UTC 2025. -Universal Time is now: Wed Apr 2 02:07:36 UTC 2025. +Local time is now: Tue May 5 09:16:00 UTC 2026. +Universal Time is now: Tue May 5 09:16:00 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-4.2) ... @@ -1687,7 +1719,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/promod3-3.4.2+ds/ && 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 > ../promod3_3.4.2+ds-1_source.changes +I: user script /srv/workspace/pbuilder/1156461/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1156461/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/promod3-3.4.2+ds/ && 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 > ../promod3_3.4.2+ds-1_source.changes dpkg-buildpackage: info: source package promod3 dpkg-buildpackage: info: source version 3.4.2+ds-1 dpkg-buildpackage: info: source distribution unstable @@ -5051,8 +5087,8 @@ Python : /usr/bin/python3 Eigen3 : /usr/include/eigen3 --- Configuring done (7.0s) --- Generating done (0.7s) +-- Configuring done (1.4s) +-- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -5068,7 +5104,7 @@ -- Build files have been written to: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' dh_auto_build - cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -5076,352 +5112,352 @@ make[2]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/depend make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/depend -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/modelling_pymod.dir/DependInfo.cmake "--color=" make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/depend -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/create_stage.dir/DependInfo.cmake "--color=" make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/depend +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/modelling_pymod.dir/DependInfo.cmake "--color=" make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/core_pymod.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/create_stage.dir/DependInfo.cmake "--color=" +make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/config/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/CMakeFiles/config_header.dir/DependInfo.cmake "--color=" -make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend +make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/depend +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/core_pymod.dir/DependInfo.cmake "--color=" +make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/depend +make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/loop_pymod.dir/DependInfo.cmake "--color=" -make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/scoring_pymod.dir/DependInfo.cmake "--color=" -make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/depend -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/depend +make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/sidechain_pymod.dir/DependInfo.cmake "--color=" -make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/build -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/__init__.py -make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/build -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake "--color=" -make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build +make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/depend +make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/__init__.py -make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/depend +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake "--color=" +make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/extras /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras/CMakeFiles/bash-completion.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/scoring/__init__.py make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/build -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/depend +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/build +make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/build +make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/loop/__init__.py -make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend +make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake "--color=" -make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/depend -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/__init__.py +make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_closegaps.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_closegaps.py -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/helper.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/scoring/__init__.py +make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/sidechain/__init__.py make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build +make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh +make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 +make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/sidechain/__init__.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.13/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-model /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data -make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_closegaps.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_closegaps.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/helper.py [ 1%] Generating ../../stage/lib64/python3.13/site-packages/promod3/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[ 1%] Generating ../stage/etc/bash_completion.d/pm-completion.bash +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/core/init/__init__.py.in -DOUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/__init__.py -DOST_COMPOUNDS_CHEMLIB_PATH="\"/var/cache/openstructure/compounds.chemlib\"" -DOST_ROOT=/usr -DPROMOD3_VERSION_STRING=3.4.2 -DGIT_BRANCH= -DGIT_COMMIT_HASH= -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-rawmodel /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/extras/pm-completion.bash.in -DOUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/etc/bash_completion.d/pm-completion.bash -DPM3_ACTION_NAMES=build-model\ build-rawmodel\ help\ build-sidechains -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/depend -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_molprobity.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_molprobity.py -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/extras /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras/CMakeFiles/bash-completion.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[ 1%] Built target scoring_pymod +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_molprobity.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_molprobity.py +[ 1%] Built target loop_pymod +[ 1%] Built target sidechain_pymod [ 1%] Built target config_header -make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/pm3argparse.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/pm3argparse.py -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_pipeline.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_pipeline.py -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.13/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data +[ 1%] Built target loop_data_dir +[ 1%] Built target sidechain_data_dir +[ 1%] Built target subst_pm +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-help /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help +make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[ 1%] Built target scoring_data_dir make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests -[ 1%] Built target scoring_pymod -[ 1%] Built target loop_data_dir -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_ring_punches.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_ring_punches.py -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_pipeline.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_pipeline.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-sidechains /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[ 1%] Built target init___init__.py_pymod +[ 1%] Built target bash-completion +make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 1%] Built target loop_pymod -make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/build +make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_ring_punches.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_ring_punches.py +[ 1%] Built target core_pymod make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 1%] Built target scoring_data_dir make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 1%] Built target subst_pm -[ 1%] Built target sidechain_pymod -[ 1%] Generating ../stage/etc/bash_completion.d/pm-completion.bash -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/extras/pm-completion.bash.in -DOUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/etc/bash_completion.d/pm-completion.bash -DPM3_ACTION_NAMES=build-model\ build-rawmodel\ help\ build-sidechains -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake -[ 1%] Built target create_stage -make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build +make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-model /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model -[ 1%] Built target init___init__.py_pymod -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_denovo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_denovo.py -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Nothing to be done for 'core/init/CMakeFiles/init_pymod.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm +[ 1%] Built target create_stage make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/depend -[ 1%] Built target sidechain_data_dir +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_denovo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_denovo.py make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/depend -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake "--color=" +[ 1%] Built target actions make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/depend make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/depend +make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake "--color=" -[ 1%] Built target bash-completion -make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_fragger_handle.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_fragger_handle.py -make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake "--color=" +[ 1%] Built target init_pymod +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_fragger_handle.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_fragger_handle.py +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/build -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-rawmodel /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel -make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./check_io.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh -[ 1%] Built target core_pymod make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/build -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/build make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build +make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./check_io.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_env.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_reconstruct_sidechains.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_reconstruct_sidechains.py -make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./cluster.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh -make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Nothing to be done for 'core/init/CMakeFiles/init_pymod.dir/build'. -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./extension_scheme.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-help /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./disulfid.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh +[ 1%] Built target promod3_scripts +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_reconstruct_sidechains.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_reconstruct_sidechains.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./cluster.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_positions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-sidechains /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./dynamic_spatial_organizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_monte_carlo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_monte_carlo.py -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./disulfid.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_monte_carlo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_monte_carlo.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./dynamic_spatial_organizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./amino_acid_atoms.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh -[ 1%] Built target init_pymod -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./export_helper.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scoring_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap_extender.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./frame.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_mhandle_helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_mhandle_helper.py -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./backbone.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./export_helper.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./model.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_alignment_fiddling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_alignment_fiddling.py -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./backbone.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scoring_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh -[ 1%] Built target actions -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap_extender.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh -[ 1%] Built target promod3_scripts -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_stems.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./bb_trace_param.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cb_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./all_atom_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_raw_model.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_raw_model.py -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./model.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_stems.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./data_bag.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./backbone_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_planar_rings.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_planar_rings.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./message.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_hash_table.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./ccd.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_planar_rings.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_planar_rings.py -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./all_atom_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cb_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_afdb_modelling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_afdb_modelling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_sink.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./backbone_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_hash_table.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_afdb_modelling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_afdb_modelling.py -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./ccd.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_source.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./kic.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_serializer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh -[ 1%] Built target modelling_pymod -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./loop_candidate.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_source.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./runtime_profiling.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./superpose.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_closer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./enumerator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./density_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./loop_candidate.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh +[ 1%] Built target modelling_pymod +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_serializer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./density_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_cooler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./runtime_profiling.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./density_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_closer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./forcefield_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_cruncher.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tree.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./superpose.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./frag_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tetrahedral_polytope.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_cooler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_density.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./enumerator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./fragger.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_group.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph_minimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_cruncher.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_density.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./rigid_blocks.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tree.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_id.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./eigen_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./rigid_blocks.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./torsion_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_group.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tetrahedral_polytope.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./score_container.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./idx_handler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph_minimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_entry.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./scoring_weights.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_scoring_function.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./loop_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_reader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./eigen_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_reconstructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./mm_system_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_connector.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./constraint_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./psipred_prediction.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh [ 1%] Built target promod3_core_headers +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./motif_finder.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/depend +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./stem_geom.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./loop_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./scoring_weights.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_id.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./mm_system_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_scoring_function.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./robin_hood.h /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/build -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_entry.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_reconstructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./psipred_prediction.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_reader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh -[ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/superpose.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/superpose.cc.o -MF CMakeFiles/promod3_core.dir/superpose.cc.o.d -o CMakeFiles/promod3_core.dir/superpose.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/superpose.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./afdb.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./afdb.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./torsion_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh [ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/cluster.cc.o +[ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o [ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o -[ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o +[ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/superpose.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/cluster.cc.o -MF CMakeFiles/promod3_core.dir/cluster.cc.o.d -o CMakeFiles/promod3_core.dir/cluster.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/cluster.cc -[ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o -MF CMakeFiles/promod3_core.dir/geom_stems.cc.o.d -o CMakeFiles/promod3_core.dir/geom_stems.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/geom_stems.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./stem_geom.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o -MF CMakeFiles/promod3_core.dir/geom_base.cc.o.d -o CMakeFiles/promod3_core.dir/geom_base.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/geom_base.cc +[ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tree.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o -MF CMakeFiles/promod3_core.dir/geom_stems.cc.o.d -o CMakeFiles/promod3_core.dir/geom_stems.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/geom_stems.cc +[ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o [ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph.cc.o -[ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tree.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph.cc.o -MF CMakeFiles/promod3_core.dir/graph.cc.o.d -o CMakeFiles/promod3_core.dir/graph.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/graph.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_connector.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh +[ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/superpose.cc.o -MF CMakeFiles/promod3_core.dir/superpose.cc.o.d -o CMakeFiles/promod3_core.dir/superpose.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/superpose.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tree.cc.o -MF CMakeFiles/promod3_core.dir/tree.cc.o.d -o CMakeFiles/promod3_core.dir/tree.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/tree.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph.cc.o -MF CMakeFiles/promod3_core.dir/graph.cc.o.d -o CMakeFiles/promod3_core.dir/graph.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/graph.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -MF CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o.d -o CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/tetrahedral_polytope.cc -[ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./motif_finder.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -MF CMakeFiles/promod3_core.dir/graph_minimizer.cc.o.d -o CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/graph_minimizer.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./constraint_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./robin_hood.h /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./torsion_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./afdb.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./afdb.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./ushort_vec.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./ushort_vec.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh -[ 5%] Built target promod3_modelling_headers -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh +[ 5%] Built target promod3_modelling_headers cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db_custom_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh -[ 5%] Built target promod3_loop_headers +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db_custom_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./subrotamer_optimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scwrl3_energy_functions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 5%] Built target promod3_scoring_headers +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[ 5%] Built target promod3_loop_headers [ 5%] Built target promod3_sidechain_headers +[ 5%] Built target promod3_scoring_headers [ 5%] Linking CXX shared library ../../stage/lib64/libpromod3_core.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_core.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_core.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_core.so.3.4 -o ../../stage/lib64/libpromod3_core.so.3.4.2 CMakeFiles/promod3_core.dir/cluster.cc.o CMakeFiles/promod3_core.dir/geom_base.cc.o CMakeFiles/promod3_core.dir/geom_stems.cc.o CMakeFiles/promod3_core.dir/superpose.cc.o CMakeFiles/promod3_core.dir/graph.cc.o CMakeFiles/promod3_core.dir/tree.cc.o CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /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 @@ -5429,63 +5465,68 @@ make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 5%] Built target promod3_core make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/depend +make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/_core.dir/DependInfo.cmake "--color=" -make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/build make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 5%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o +[ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o +[ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o [ 7%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o -[ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_geom.cc.o +[ 7%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o +[ 7%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o -MF CMakeFiles/promod3_loop.dir/all_atom_env.cc.o.d -o CMakeFiles/promod3_loop.dir/all_atom_env.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/all_atom_env.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_geom.cc.o -MF CMakeFiles/_core.dir/export_geom.cc.o.d -o CMakeFiles/_core.dir/export_geom.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/export_geom.cc -[ 8%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -[ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o -MF CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o.d -o CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/all_atom_positions.cc -[ 9%] Building CXX object core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -MF CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o.d -o CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/amino_acid_atoms.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o -MF CMakeFiles/_core.dir/wrap_core.cc.o.d -o CMakeFiles/_core.dir/wrap_core.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/wrap_core.cc -[ 11%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_graph_minimizer.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o -MF CMakeFiles/promod3_loop.dir/density_creator.cc.o.d -o CMakeFiles/promod3_loop.dir/density_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/density_creator.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_graph_minimizer.cc.o -MF CMakeFiles/_core.dir/export_graph_minimizer.cc.o.d 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/forcefield_lookup.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong 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-ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o -MF CMakeFiles/promod3_loop.dir/backbone.cc.o.d -o CMakeFiles/promod3_loop.dir/backbone.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/backbone.cc +[ 8%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/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_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o -MF CMakeFiles/_core.dir/wrap_core.cc.o.d -o CMakeFiles/_core.dir/wrap_core.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/wrap_core.cc +[ 8%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o -MF CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o.d -o CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/bb_trace_param.cc -[ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o -MF CMakeFiles/promod3_loop.dir/frag_db.cc.o.d -o CMakeFiles/promod3_loop.dir/frag_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/frag_db.cc -[ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o +[ 8%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB 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loop/src/CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o -MF CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o.d -o CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/hydrogen_constructor.cc -[ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/idx_handler.cc.o -[ 14%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection 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-Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o -MF CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o.d -o CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/mm_system_creator.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o -[ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/structure_db.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK 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CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/sidechain_atom_constructor.cc +[ 19%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/core/_core.so +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_core.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_core.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/core/_core.so CMakeFiles/_core.dir/export_geom.cc.o CMakeFiles/_core.dir/export_runtime_profiling.cc.o CMakeFiles/_core.dir/export_graph_minimizer.cc.o CMakeFiles/_core.dir/wrap_core.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /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 +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[ 19%] Built target _core 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, @@ -5584,11 +5625,6 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -[ 19%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/core/_core.so -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_core.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_core.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/core/_core.so CMakeFiles/_core.dir/export_geom.cc.o CMakeFiles/_core.dir/export_runtime_profiling.cc.o CMakeFiles/_core.dir/export_graph_minimizer.cc.o CMakeFiles/_core.dir/wrap_core.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /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 -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 19%] Built target _core [ 19%] Linking CXX shared library ../../stage/lib64/libpromod3_loop.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_loop.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_loop.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_loop.so.3.4 -o ../../stage/lib64/libpromod3_loop.so.3.4.2 CMakeFiles/promod3_loop.dir/all_atom_env.cc.o CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o CMakeFiles/promod3_loop.dir/backbone.cc.o CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o CMakeFiles/promod3_loop.dir/density_creator.cc.o CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o CMakeFiles/promod3_loop.dir/frag_db.cc.o CMakeFiles/promod3_loop.dir/fragger.cc.o CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o CMakeFiles/promod3_loop.dir/idx_handler.cc.o CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o CMakeFiles/promod3_loop.dir/structure_db.cc.o CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /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 @@ -5605,194 +5641,132 @@ make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: 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'/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[ 21%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_all_atom_env.cc.o [ 21%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o +[ 21%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o +[ 22%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -MF CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o.d -o CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/scoring_object_loader.cc -[ 26%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -[ 26%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o -[ 26%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o -MF CMakeFiles/promod3_sidechain.dir/frame.cc.o.d -o CMakeFiles/promod3_sidechain.dir/frame.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/frame.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o -MF CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o.d -o CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_amino_acid_atoms.cc +[ 26%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/bb_dep_rotamer_lib.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK 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/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/cbeta_env_listener.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o -MF CMakeFiles/_loop.dir/export_backbone.cc.o.d -o CMakeFiles/_loop.dir/export_backbone.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_backbone.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -MF CMakeFiles/promod3_sidechain.dir/disulfid.cc.o.d -o CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/disulfid.cc -[ 28%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o +[ 29%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o +[ 29%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/particle_scoring.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/cbeta_score.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o -MF CMakeFiles/promod3_sidechain.dir/frame.cc.o.d -o CMakeFiles/promod3_sidechain.dir/frame.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/frame.cc -[ 29%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -MF CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o.d -o CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_forcefield_lookup.cc +[ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o +[ 35%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o +[ 35%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o -MF CMakeFiles/_loop.dir/export_frag_db.cc.o.d -o CMakeFiles/_loop.dir/export_frag_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_frag_db.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o -MF CMakeFiles/_loop.dir/export_fragger.cc.o.d -o CMakeFiles/_loop.dir/export_fragger.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_fragger.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/reduced_env_listener.cc -[ 29%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/particle_scoring.cc -[ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -[ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -c 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/build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_frag_db.cc +[ 32%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o +[ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o +[ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o +[ 32%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o +[ 32%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o +[ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o +[ 32%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o +[ 32%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK 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loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o +[ 39%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o +[ 39%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o +[ 38%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 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-DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_cruncher.cc -[ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -MF CMakeFiles/_loop.dir/export_psipred_prediction.cc.o.d -o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_psipred_prediction.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o -MF CMakeFiles/_loop.dir/export_structure_db.cc.o.d -o CMakeFiles/_loop.dir/export_structure_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_structure_db.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -MF 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loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -MF CMakeFiles/_loop.dir/export_torsion_sampler.cc.o.d -o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_torsion_sampler.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o -MF CMakeFiles/_loop.dir/wrap_loop.cc.o.d -o CMakeFiles/_loop.dir/wrap_loop.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/wrap_loop.cc +[ 42%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_group.cc -[ 33%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_id.cc -[ 33%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib.cc -[ 35%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o +[ 42%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/reduced_score.cc -[ 35%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o +[ 43%] Building CXX object 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib_reader.cc -[ 38%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/sidechain_connector.cc -[ 38%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o +[ 43%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/clash_score.cc -[ 39%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK 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sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o.d -o 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scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/hbond_env_listener.cc -[ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lookup.cc -[ 42%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/hbond_score.cc -[ 42%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl4_rotamer_constructor.cc -[ 42%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o -MF CMakeFiles/_loop.dir/export_fragger.cc.o.d -o CMakeFiles/_loop.dir/export_fragger.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_fragger.cc -[ 43%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/vina_rotamer_constructor.cc -[ 43%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/ss_agreement_score.cc -[ 45%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -MF CMakeFiles/_loop.dir/export_loop_object_loader.cc.o.d -o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_loop_object_loader.cc -[ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/ss_agreement_env_listener.cc -[ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -MF CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/subrotamer_optimizer.cc -[ 46%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/ss_agreement_score.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib_entry.cc +[ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -MF CMakeFiles/promod3_scoring.dir/torsion_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/torsion_score.cc +[ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib_reader.cc +[ 46%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/sidechain_connector.cc [ 46%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -MF CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/pairwise_score.cc [ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -MF CMakeFiles/_loop.dir/export_mm_system_creator.cc.o.d -o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_mm_system_creator.cc -[ 49%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -MF CMakeFiles/_loop.dir/export_psipred_prediction.cc.o.d -o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_psipred_prediction.cc -[ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o +[ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_overall_scorer.cc -[ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o +[ 47%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/sidechain_object_loader.cc +[ 47%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_constructor.cc +[ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_interaction_env_listener.cc -[ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o +[ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_interaction_score.cc -[ 50%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o -MF CMakeFiles/_loop.dir/export_structure_db.cc.o.d -o CMakeFiles/_loop.dir/export_structure_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_structure_db.cc -[ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o +[ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_packing_score.cc +[ 50%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lookup.cc [ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_clash_score.cc -[ 52%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -MF CMakeFiles/_loop.dir/export_torsion_sampler.cc.o.d -o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_torsion_sampler.cc -[ 53%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o -MF CMakeFiles/_loop.dir/wrap_loop.cc.o.d -o CMakeFiles/_loop.dir/wrap_loop.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/wrap_loop.cc -[ 54%] Linking CXX shared library ../../stage/lib64/libpromod3_sidechain.so -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_sidechain.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_sidechain.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_sidechain.so.3.4 -o ../../stage/lib64/libpromod3_sidechain.so.3.4.2 CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o CMakeFiles/promod3_sidechain.dir/disulfid.cc.o CMakeFiles/promod3_sidechain.dir/frame.cc.o CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/rotamer.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_sidechain.so.3.4 ../../stage/lib64/libpromod3_sidechain.so -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 54%] Built target promod3_sidechain -make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/depend -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake "--color=" -[ 54%] Linking CXX shared library ../../stage/lib64/libpromod3_scoring.so -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_scoring.dir/link.txt --verbose=1 -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/build -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 54%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_connector.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_connector.cc.o -MF CMakeFiles/_sidechain.dir/export_connector.cc.o.d -o CMakeFiles/_sidechain.dir/export_connector.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_connector.cc -[ 56%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_disulfid.cc.o -[ 57%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /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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CMakeFiles/_sidechain.dir/export_particle.cc.o.d -o CMakeFiles/_sidechain.dir/export_particle.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_particle.cc -[ 59%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 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-I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl3_rotamer_constructor.cc +[ 53%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB 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/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -MF CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/subrotamer_optimizer.cc In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, @@ -5811,72 +5785,122 @@ /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:66:32: note: '' declared here 66 | v.push_back(boost::python::extract(l[i])); | ^~~~~~~~~~~~~~~~ -[ 66%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include 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/usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_scoring.so.3.4 ../../stage/lib64/libpromod3_scoring.so +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[ 53%] Built target promod3_scoring +make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/depend +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod 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-DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o -MF CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o.d -o CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_pairwise_functions.cc -[ 70%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -MF CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o.d -o CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/backbone_relaxer.cc -[ 70%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o +[ 57%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_backbone_score.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o -MF CMakeFiles/_scoring.dir/wrap_scoring.cc.o.d -o CMakeFiles/_scoring.dir/wrap_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/wrap_scoring.cc +[ 60%] Linking CXX shared library ../../stage/lib64/libpromod3_sidechain.so +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_sidechain.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_sidechain.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_sidechain.so.3.4 -o ../../stage/lib64/libpromod3_sidechain.so.3.4.2 CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o CMakeFiles/promod3_sidechain.dir/disulfid.cc.o CMakeFiles/promod3_sidechain.dir/frame.cc.o CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/rotamer.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_sidechain.so.3.4 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-DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_connector.cc.o -MF CMakeFiles/_sidechain.dir/export_connector.cc.o.d -o CMakeFiles/_sidechain.dir/export_connector.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_connector.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK 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/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_disulfid.cc.o -MF CMakeFiles/_sidechain.dir/export_disulfid.cc.o.d -o CMakeFiles/_sidechain.dir/export_disulfid.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_disulfid.cc +[ 70%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_frame.cc.o -MF CMakeFiles/_sidechain.dir/export_frame.cc.o.d -o CMakeFiles/_sidechain.dir/export_frame.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_frame.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/model.cc.o -MF CMakeFiles/promod3_modelling.dir/model.cc.o.d -o CMakeFiles/promod3_modelling.dir/model.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/model.cc +[ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_graph.cc +[ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o -MF CMakeFiles/promod3_modelling.dir/ccd.cc.o.d -o CMakeFiles/promod3_modelling.dir/ccd.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/ccd.cc -[ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o +[ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_particle.cc.o -MF CMakeFiles/_sidechain.dir/export_particle.cc.o.d -o CMakeFiles/_sidechain.dir/export_particle.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_particle.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o -MF CMakeFiles/promod3_modelling.dir/kic.cc.o.d -o CMakeFiles/promod3_modelling.dir/kic.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/kic.cc -[ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -MF CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o.d -o CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/loop_candidate.cc -[ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo.cc -[ 71%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && 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object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer.cc +[ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_closer.cc -[ 73%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_ids.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -MF CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o.d -o CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_sidechain_object_loader.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_scorer.cc +[ 76%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o +[ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o +[ 77%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_constructor.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_sampler.cc -/build/reproducible-path/promod3-3.4.2+ds/modelling/src/model.cc: In function 'void promod3::modelling::MergeMHandle(const ModellingHandle&, ModellingHandle&, uint, uint, uint, uint, const geom::Mat4&)': -/build/reproducible-path/promod3-3.4.2+ds/modelling/src/model.cc:402:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 402 | const String& seqres = source_mhandle.seqres[source_chain_idx].GetString(); - | ^~~~~~ -/build/reproducible-path/promod3-3.4.2+ds/modelling/src/model.cc:402:75: note: the temporary was destroyed at the end of the full expression 'ost::seq::SequenceList::operator[](int) const(((int)source_chain_idx)).ost::seq::SequenceHandle::GetString()' - 402 | const String& seqres = source_mhandle.seqres[source_chain_idx].GetString(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -[ 74%] Linking 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/build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/wrap_sidechain.cc +[ 80%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -MF 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CMakeFiles/_loop.dir/export_frag_db.cc.o CMakeFiles/_loop.dir/export_fragger.cc.o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o CMakeFiles/_loop.dir/export_structure_db.cc.o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o CMakeFiles/_loop.dir/wrap_loop.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_loop.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /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 -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 74%] Built target _loop -[ 76%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o -MF CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o.d -o CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_scwrl3_energy_functions.cc -[ 76%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB 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/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o -MF CMakeFiles/promod3_modelling.dir/score_container.cc.o.d -o CMakeFiles/promod3_modelling.dir/score_container.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/score_container.cc -[ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -MF CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o.d -o CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/scoring_weights.cc -[ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o +[ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -MF CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o.d -o CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/backbone_relaxer.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -MF CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o.d -o CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/scoring_weights.cc +[ 81%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/motif_finder.cc.o +[ 81%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o +[ 81%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/afdb.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o -MF CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o.d -o CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/sidechain_env_listener.cc -[ 80%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/motif_finder.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/motif_finder.cc.o -MF CMakeFiles/promod3_modelling.dir/motif_finder.cc.o.d -o CMakeFiles/promod3_modelling.dir/motif_finder.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/motif_finder.cc -[ 80%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/afdb.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/afdb.cc.o -MF CMakeFiles/promod3_modelling.dir/afdb.cc.o.d -o CMakeFiles/promod3_modelling.dir/afdb.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/afdb.cc -[ 81%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o -MF CMakeFiles/_scoring.dir/wrap_scoring.cc.o.d -o CMakeFiles/_scoring.dir/wrap_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/wrap_scoring.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/motif_finder.cc.o -MF CMakeFiles/promod3_modelling.dir/motif_finder.cc.o.d -o CMakeFiles/promod3_modelling.dir/motif_finder.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/motif_finder.cc /build/reproducible-path/promod3-3.4.2+ds/modelling/src/afdb.cc: In function 'void promod3::modelling::CreatePentaMatch(const ost::seq::SequenceList&, const String&, bool)': /build/reproducible-path/promod3-3.4.2+ds/modelling/src/afdb.cc:220:21: warning: possibly dangling reference to a temporary [-Wdangling-reference] 220 | const String& sname = seq_list[i].GetName(); @@ -5884,16 +5908,23 @@ /build/reproducible-path/promod3-3.4.2+ds/modelling/src/afdb.cc:220:48: note: the temporary was destroyed at the end of the full expression 'ost::seq::SequenceList::operator[](int) const(i).ost::seq::SequenceHandle::GetName()' 220 | const String& sname = seq_list[i].GetName(); | ~~~~~~~~~~~~~~~~~~~^~ +[ 81%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/loop/_loop.so +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_loop.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_loop.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/loop/_loop.so CMakeFiles/_loop.dir/export_all_atom_env.cc.o CMakeFiles/_loop.dir/export_all_atom_positions.cc.o CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o CMakeFiles/_loop.dir/export_backbone.cc.o CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o CMakeFiles/_loop.dir/export_frag_db.cc.o CMakeFiles/_loop.dir/export_fragger.cc.o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o CMakeFiles/_loop.dir/export_structure_db.cc.o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o CMakeFiles/_loop.dir/wrap_loop.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_loop.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /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 +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[ 81%] Built target _loop +/build/reproducible-path/promod3-3.4.2+ds/modelling/src/model.cc: In function 'void promod3::modelling::MergeMHandle(const ModellingHandle&, ModellingHandle&, uint, uint, uint, uint, const geom::Mat4&)': +/build/reproducible-path/promod3-3.4.2+ds/modelling/src/model.cc:402:17: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 402 | const String& seqres = source_mhandle.seqres[source_chain_idx].GetString(); + | ^~~~~~ +/build/reproducible-path/promod3-3.4.2+ds/modelling/src/model.cc:402:75: note: the temporary was destroyed at the end of the full expression 'ost::seq::SequenceList::operator[](int) const(((int)source_chain_idx)).ost::seq::SequenceHandle::GetString()' + 402 | const String& seqres = source_mhandle.seqres[source_chain_idx].GetString(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ [ 81%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/scoring/_scoring.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_scoring.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_scoring.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/scoring/_scoring.so CMakeFiles/_scoring.dir/export_backbone_score.cc.o CMakeFiles/_scoring.dir/export_all_atom_score.cc.o CMakeFiles/_scoring.dir/export_object_loader.cc.o CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o CMakeFiles/_scoring.dir/export_density_scorer.cc.o CMakeFiles/_scoring.dir/wrap_scoring.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_scoring.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 81%] Built target _scoring -[ 81%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_sidechain.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_sidechain.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so CMakeFiles/_sidechain.dir/export_connector.cc.o CMakeFiles/_sidechain.dir/export_disulfid.cc.o CMakeFiles/_sidechain.dir/export_frame.cc.o CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o CMakeFiles/_sidechain.dir/export_particle.cc.o CMakeFiles/_sidechain.dir/export_rotamer.cc.o CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_sidechain.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 81%] Built target _sidechain In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/eigen_types.hh:23, @@ -5926,6 +5957,11 @@ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 4 of type 'const double*' 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 = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 81%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_sidechain.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_sidechain.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so CMakeFiles/_sidechain.dir/export_connector.cc.o CMakeFiles/_sidechain.dir/export_disulfid.cc.o CMakeFiles/_sidechain.dir/export_frame.cc.o 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/usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[ 81%] Built target _sidechain [ 81%] Linking CXX shared library ../../stage/lib64/libpromod3_modelling.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_modelling.dir/link.txt 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/usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 @@ -5939,32 +5975,32 @@ make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 83%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_extension_scheme.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat 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85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap.cc.o [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_model.cc.o +[ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_closure.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG 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-I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_loop_closure.cc.o -MF CMakeFiles/_modelling.dir/export_loop_closure.cc.o.d -o CMakeFiles/_modelling.dir/export_loop_closure.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_loop_closure.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/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_SYSTEM_DYN_LINK 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-I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -MF CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o.d -o CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_rigid_blocks.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/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_SYSTEM_DYN_LINK 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o -MF CMakeFiles/_modelling.dir/wrap_modelling.cc.o.d -o CMakeFiles/_modelling.dir/wrap_modelling.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/wrap_modelling.cc [ 90%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/modelling/_modelling.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_modelling.dir/link.txt --verbose=1 @@ -5983,148 +6019,145 @@ make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/depend +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && 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-make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/depend -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/depend +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/DependInfo.cmake "--color=" make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/depend -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/depend -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/depend -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/DependInfo.cmake "--color=" -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build +make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/depend -make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/depend -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/DependInfo.cmake "--color=" +make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/depend +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/DependInfo.cmake "--color=" -[ 91%] Generating ../../stage/share/promod3/loop_data/ff_lookup_charmm.dat -[ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_coil.dat +make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_coil.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_coil.dat'\ TorsionSampler -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/depend +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/DependInfo.cmake "--color=" +make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/depend +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/DependInfo.cmake "--color=" +make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_ff_lookup_charmm.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/ff_lookup_charmm.dat'\ ForcefieldLookup -make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler.dat +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler.dat'\ TorsionSampler -[ 92%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_extended.dat +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_extended.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_extended.dat'\ TorsionSampler make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build +make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 92%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_helical.dat -make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 92%] Generating ../../stage/share/promod3/loop_data/frag_db.dat +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_frag_db.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/frag_db.dat'\ FragDB -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_helical.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_helical.dat'\ TorsionSampler -make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/depend -make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/depend -[ 94%] Generating ../../stage/share/promod3/loop_data/structure_db.dat -[ 95%] Generating ../../stage/share/promod3/scoring_data/aa_packing_scorer.dat +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build +make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build +make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build +make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_structure_db.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/structure_db.dat'\ StructureDB -make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/depend -[ 95%] Generating ../../stage/share/promod3/scoring_data/cb_packing_scorer.dat -make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/depend -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_aa_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_packing_scorer.dat'\ AllAtomPackingScorer -make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/DependInfo.cmake "--color=" -make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/depend -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_cb_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cb_packing_scorer.dat'\ CBPackingScorer +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/DependInfo.cmake "--color=" -[ 97%] Generating ../../stage/share/promod3/scoring_data/reduced_scorer.dat -[ 98%] Generating ../../stage/share/promod3/scoring_data/cbeta_scorer.dat -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_reduced_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/reduced_scorer.dat'\ ReducedScorer -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_cbeta_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cbeta_scorer.dat'\ CBetaScorer make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build +make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -Compound library not available. Some functionality may not work as expected. -Compound library not available. Some functionality may not work as expected. -Compound library not available. Some functionality may not work as expected. +make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[ 90%] Generating ../../stage/share/promod3/loop_data/torsion_sampler.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -Compound library not available. Some functionality may not work as expected. -make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -Compound library not available. Some functionality may not work as expected. -Compound library not available. Some functionality may not work as expected. +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler.dat'\ TorsionSampler +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build +[ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_extended.dat make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -Compound library not available. Some functionality may not work as expected. +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_extended.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_extended.dat'\ TorsionSampler make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build +[ 92%] Generating ../../stage/share/promod3/loop_data/ff_lookup_charmm.dat +[ 92%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_coil.dat make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -Compound library not available. Some functionality may not work as expected. +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_ff_lookup_charmm.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/ff_lookup_charmm.dat'\ ForcefieldLookup +[ 94%] Generating ../../stage/share/promod3/scoring_data/reduced_scorer.dat +[ 94%] Generating ../../stage/share/promod3/loop_data/frag_db.dat +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_coil.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_coil.dat'\ TorsionSampler +[ 94%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_helical.dat +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_reduced_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/reduced_scorer.dat'\ ReducedScorer +[ 95%] Generating ../../stage/share/promod3/scoring_data/aa_packing_scorer.dat +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_frag_db.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/frag_db.dat'\ FragDB +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_helical.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_helical.dat'\ TorsionSampler +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_aa_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_packing_scorer.dat'\ AllAtomPackingScorer +[ 97%] Generating ../../stage/share/promod3/scoring_data/cbeta_scorer.dat +[ 97%] Generating ../../stage/share/promod3/scoring_data/aa_scorer.dat +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_cbeta_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cbeta_scorer.dat'\ CBetaScorer +[ 98%] Generating ../../stage/share/promod3/loop_data/structure_db.dat +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_aa_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_scorer.dat'\ AllAtomInteractionScorer +[ 98%] Generating ../../stage/share/promod3/scoring_data/cb_packing_scorer.dat +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_structure_db.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/structure_db.dat'\ StructureDB +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_cb_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cb_packing_scorer.dat'\ CBPackingScorer [ 98%] Generating ../../stage/share/promod3/scoring_data/hbond_scorer.dat -Compound library not available. Some functionality may not work as expected. -make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_hbond_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/hbond_scorer.dat'\ HBondScorer +[100%] Generating ../../stage/share/promod3/sidechain_data/bb_dep_lib.dat +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/portable_bb_dep_lib.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/bb_dep_lib.dat'\ BBDepRotamerLib +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 98%] Generating ../../stage/share/promod3/scoring_data/ss_agreement_scorer.dat -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_ss_agreement_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/ss_agreement_scorer.dat'\ SSAgreementScorer Compound library not available. Some functionality may not work as expected. -[ 98%] Generating ../../stage/share/promod3/scoring_data/torsion_scorer.dat -[ 98%] Generating ../../stage/share/promod3/scoring_data/aa_scorer.dat +[100%] Generating ../../stage/share/promod3/scoring_data/ss_agreement_scorer.dat +[100%] Generating ../../stage/share/promod3/scoring_data/torsion_scorer.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_torsion_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/torsion_scorer.dat'\ TorsionScorer -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_aa_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_scorer.dat'\ AllAtomInteractionScorer +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_ss_agreement_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/ss_agreement_scorer.dat'\ SSAgreementScorer +Compound library not available. Some functionality may not work as expected. +Compound library not available. Some functionality may not work as expected. +Compound library not available. Some functionality may not work as expected. +Compound library not available. Some functionality may not work as expected. +Compound library not available. Some functionality may not work as expected. +Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. -[100%] Generating ../../stage/share/promod3/sidechain_data/bb_dep_lib.dat -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/portable_bb_dep_lib.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/bb_dep_lib.dat'\ BBDepRotamerLib [100%] Generating ../../stage/share/promod3/sidechain_data/lib.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/portable_lib.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/lib.dat'\ RotamerLib Compound library not available. Some functionality may not work as expected. @@ -6133,6 +6166,9 @@ Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. +Compound library not available. Some functionality may not work as expected. +Compound library not available. Some functionality may not work as expected. +Compound library not available. Some functionality may not work as expected. /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' @@ -6149,36 +6185,29 @@ pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" -/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' - pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" -/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' - pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[100%] Built target generate_scoring_data_cbeta_scorer.dat -[100%] Built target generate_scoring_data_aa_packing_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[100%] Built target generate_sidechain_data_lib.dat [100%] Built target generate_scoring_data_cb_packing_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[100%] Built target generate_scoring_data_torsion_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[100%] Built target generate_scoring_data_ss_agreement_scorer.dat +[100%] Built target generate_scoring_data_aa_packing_scorer.dat +[100%] Built target generate_sidechain_data_lib.dat [100%] Built target generate_scoring_data_aa_scorer.dat -[100%] Built target generate_scoring_data_torsion_scorer.dat +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[100%] Built target generate_scoring_data_reduced_scorer.dat [100%] Built target generate_loop_data_ff_lookup_charmm.dat -[100%] Built target generate_scoring_data_hbond_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[100%] Built target generate_loop_data_torsion_sampler_extended.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[100%] Built target generate_scoring_data_hbond_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[100%] Built target generate_loop_data_torsion_sampler_coil.dat -[100%] Built target generate_loop_data_torsion_sampler.dat +[100%] Built target generate_loop_data_torsion_sampler_helical.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[100%] Built target generate_scoring_data_reduced_scorer.dat +[100%] Built target generate_scoring_data_cbeta_scorer.dat +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[100%] Built target generate_scoring_data_ss_agreement_scorer.dat make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake "--color=" @@ -6188,13 +6217,16 @@ make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'scoring/data/CMakeFiles/scoring_data.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[100%] Built target generate_loop_data_torsion_sampler_helical.dat +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target scoring_data make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[100%] Built target generate_loop_data_torsion_sampler_coil.dat [100%] Built target generate_sidechain_data_bb_dep_lib.dat +[100%] Built target generate_loop_data_torsion_sampler_extended.dat make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data.dir/DependInfo.cmake "--color=" +[100%] Built target generate_loop_data_torsion_sampler.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -6451,7 +6483,7 @@ Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- -Ran 2 tests in 0.728s +Ran 2 tests in 0.178s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -6467,7 +6499,7 @@ Compound library not available. Some functionality may not work as expected. ............ ---------------------------------------------------------------------- -Ran 12 tests in 0.012s +Ran 12 tests in 0.004s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -6483,7 +6515,7 @@ Compound library not available. Some functionality may not work as expected. .................................................................. ---------------------------------------------------------------------- -Ran 66 tests in 10.214s +Ran 66 tests in 3.740s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7319,7 +7351,7 @@ Compound library not available. Some functionality may not work as expected. ................................. ---------------------------------------------------------------------- -Ran 33 tests in 67.356s +Ran 33 tests in 21.848s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7335,7 +7367,7 @@ Compound library not available. Some functionality may not work as expected. ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.125s +Ran 6 tests in 0.022s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7354,7 +7386,7 @@ residue A.GLY8 is missing atoms CA ........ ---------------------------------------------------------------------- -Ran 25 tests in 0.374s +Ran 25 tests in 0.113s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7371,7 +7403,7 @@ Switched to slower reference platform of OpenMM! ............... ---------------------------------------------------------------------- -Ran 15 tests in 124.554s +Ran 15 tests in 40.709s OK OpenMM CPU platform not available. Skipping almost_on_top check. @@ -7389,7 +7421,7 @@ Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- -Ran 2 tests in 0.373s +Ran 2 tests in 0.130s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7405,7 +7437,7 @@ Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- -Ran 2 tests in 6.322s +Ran 2 tests in 2.233s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7421,7 +7453,7 @@ Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- -Ran 2 tests in 0.033s +Ran 2 tests in 0.012s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7456,7 +7488,7 @@ Compound library not available. Some functionality may not work as expected. ... ---------------------------------------------------------------------- -Ran 3 tests in 12.136s +Ran 3 tests in 4.898s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7472,7 +7504,7 @@ Compound library not available. Some functionality may not work as expected. ... ---------------------------------------------------------------------- -Ran 3 tests in 4.251s +Ran 3 tests in 1.359s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7488,7 +7520,7 @@ Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- -Ran 2 tests in 0.089s +Ran 2 tests in 0.032s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7519,7 +7551,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/promod3-3.4.2\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/promod3-3.4.2\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -7743,11 +7775,11 @@ dh_installdocs dh_installchangelogs dh_python3 -I: dh_python3 fs:421: renaming _core.so to _core.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming _sidechain.so to _sidechain.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _loop.so to _loop.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming _scoring.so to _scoring.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _modelling.so to _modelling.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming _sidechain.so to _sidechain.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming _core.so to _core.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming _scoring.so to _scoring.cpython-313-x86_64-linux-gnu.so dh_perl dh_link dh_strip_nondeterminism @@ -7763,25 +7795,25 @@ dpkg-gencontrol: warning: Depends field of package promod3: substitution variable ${python3:Depends} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libpromod3-loop3.4-dbgsym' in '../libpromod3-loop3.4-dbgsym_3.4.2+ds-1_amd64.deb'. -dpkg-deb: building package 'libpromod3-loop-dev' in '../libpromod3-loop-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-core-dev' in '../libpromod3-core-dev_3.4.2+ds-1_amd64.deb'. -dpkg-deb: building package 'libpromod3-core3.4-dbgsym' in '../libpromod3-core3.4-dbgsym_3.4.2+ds-1_amd64.deb'. -dpkg-deb: building package 'libpromod3-scoring3.4' in '../libpromod3-scoring3.4_3.4.2+ds-1_amd64.deb'. -dpkg-deb: building package 'libpromod3-sidechain-dev' in '../libpromod3-sidechain-dev_3.4.2+ds-1_amd64.deb'. -dpkg-deb: building package 'libpromod3-modelling3.4-dbgsym' in '../libpromod3-modelling3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.4' in '../libpromod3-core3.4_3.4.2+ds-1_amd64.deb'. -dpkg-deb: building package 'promod3-data' in '../promod3-data_3.4.2+ds-1_all.deb'. -dpkg-deb: building package 'libpromod3-modelling3.4' in '../libpromod3-modelling3.4_3.4.2+ds-1_amd64.deb'. +dpkg-deb: building package 'libpromod3-core3.4-dbgsym' in '../libpromod3-core3.4-dbgsym_3.4.2+ds-1_amd64.deb'. +dpkg-deb: building package 'libpromod3-loop-dev' in '../libpromod3-loop-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop3.4' in '../libpromod3-loop3.4_3.4.2+ds-1_amd64.deb'. -dpkg-deb: building package 'libpromod3-sidechain3.4' in '../libpromod3-sidechain3.4_3.4.2+ds-1_amd64.deb'. -dpkg-deb: building package 'python3-promod3-dbgsym' in '../python3-promod3-dbgsym_3.4.2+ds-1_amd64.deb'. -dpkg-deb: building package 'python3-promod3' in '../python3-promod3_3.4.2+ds-1_amd64.deb'. +dpkg-deb: building package 'libpromod3-loop3.4-dbgsym' in '../libpromod3-loop3.4-dbgsym_3.4.2+ds-1_amd64.deb'. +dpkg-deb: building package 'libpromod3-modelling3.4' in '../libpromod3-modelling3.4_3.4.2+ds-1_amd64.deb'. +dpkg-deb: building package 'libpromod3-modelling3.4-dbgsym' in '../libpromod3-modelling3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling-dev' in '../libpromod3-modelling-dev_3.4.2+ds-1_amd64.deb'. -dpkg-deb: building package 'promod3' in '../promod3_3.4.2+ds-1_all.deb'. -dpkg-deb: building package 'libpromod3-sidechain3.4-dbgsym' in '../libpromod3-sidechain3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-scoring-dev' in '../libpromod3-scoring-dev_3.4.2+ds-1_amd64.deb'. +dpkg-deb: building package 'libpromod3-scoring3.4' in '../libpromod3-scoring3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-scoring3.4-dbgsym' in '../libpromod3-scoring3.4-dbgsym_3.4.2+ds-1_amd64.deb'. +dpkg-deb: building package 'libpromod3-sidechain-dev' in '../libpromod3-sidechain-dev_3.4.2+ds-1_amd64.deb'. +dpkg-deb: building package 'libpromod3-sidechain3.4' in '../libpromod3-sidechain3.4_3.4.2+ds-1_amd64.deb'. +dpkg-deb: building package 'libpromod3-sidechain3.4-dbgsym' in '../libpromod3-sidechain3.4-dbgsym_3.4.2+ds-1_amd64.deb'. +dpkg-deb: building package 'promod3' in '../promod3_3.4.2+ds-1_all.deb'. +dpkg-deb: building package 'promod3-data' in '../promod3-data_3.4.2+ds-1_all.deb'. +dpkg-deb: building package 'python3-promod3' in '../python3-promod3_3.4.2+ds-1_amd64.deb'. +dpkg-deb: building package 'python3-promod3-dbgsym' in '../python3-promod3-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../promod3_3.4.2+ds-1_amd64.buildinfo dpkg-genchanges --build=binary -O../promod3_3.4.2+ds-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -7789,12 +7821,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1156461/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1156461/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/899332 and its subdirectories -I: Current time: Tue Apr 1 14:50:42 -12 2025 -I: pbuilder-time-stamp: 1743562242 +I: removing directory /srv/workspace/pbuilder/1156461 and its subdirectories +I: Current time: Tue May 5 23:27:46 +14 2026 +I: pbuilder-time-stamp: 1777973266