Diff of the two buildlogs: -- --- b1/build.log 2025-10-17 13:56:48.123497083 +0000 +++ b2/build.log 2025-10-17 14:00:40.375763361 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Nov 19 08:17:47 -12 2026 -I: pbuilder-time-stamp: 1795119467 +I: Current time: Sat Oct 18 03:57:04 +14 2025 +I: pbuilder-time-stamp: 1760709424 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ dpkg-source: info: applying 968a0af8bc1a224337a3d1e1bd2fec3aec9e3fa1.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/219889/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2133002/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-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 Oct 17 13:58 /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/2133002/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2133002/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=16 ' - DISTRIBUTION='forky' - 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='74a3d7ccbef647c2a3d8d759acf55cff' - 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='219889' - PS1='# ' - PS2='> ' + INVOCATION_ID=3709bb03013b4c5abc71fc0de7fab738 + 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=2133002 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.cgCG2yJv/pbuilderrc_Qaa5 --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cgCG2yJv/b1 --logfile b1/build.log molmodel_3.1.0-4.1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.cgCG2yJv/pbuilderrc_NkHP --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cgCG2yJv/b2 --logfile b2/build.log molmodel_3.1.0-4.1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/219889/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2133002/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -265,7 +297,7 @@ Get: 139 http://deb.debian.org/debian forky/main amd64 libsimbody3.7 amd64 3.7+dfsg-5 [3393 kB] Get: 140 http://deb.debian.org/debian forky/main amd64 libsimbody-dev amd64 3.7+dfsg-5 [2727 kB] Get: 141 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 116 MB in 2s (61.3 MB/s) +Fetched 116 MB in 3s (42.9 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 19898 files and directories currently installed.) @@ -852,7 +884,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/molmodel-3.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../molmodel_3.1.0-4.1_source.changes +I: user script /srv/workspace/pbuilder/2133002/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2133002/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/molmodel-3.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../molmodel_3.1.0-4.1_source.changes dpkg-buildpackage: info: source package molmodel dpkg-buildpackage: info: source version 3.1.0-4.1 dpkg-buildpackage: info: source distribution unstable @@ -900,7 +936,7 @@ This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) --- Configuring done (0.6s) +-- Configuring done (0.8s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -913,7 +949,7 @@ -- Build files have been written to: /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/molmodel-3.1.0' dh_auto_build - cd obj-x86_64-linux-gnu && make -j16 INSTALL="install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j12 INSTALL="install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/molmodel-3.1.0 -B/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -925,44 +961,34 @@ make[3]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' make -f CMakeFiles/SimTKmolmodel.dir/build.make CMakeFiles/SimTKmolmodel.dir/build make[3]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' -[ 3%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/About.cpp.o -[ 6%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Biotype.cpp.o +[ 3%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Biotype.cpp.o +[ 6%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o +[ 9%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o +/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/AtomSubsystem.cpp +[ 15%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/About.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/Biotype.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/Biotype.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/Biotype.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/Biotype.cpp -[ 12%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Compound.cpp.o -[ 12%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o -[ 18%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o -[ 18%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o -[ 25%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o -[ 25%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o -[ 28%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o -[ 31%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o +/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/BondGeometry.cpp +[ 18%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o +[ 12%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystem.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/About.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/About.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/About.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/About.cpp -[ 34%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystem.cpp.o -[ 37%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o -/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/AtomSubsystem.cpp +/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystem.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystem.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystem.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp +[ 21%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o +/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp +/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/Element.cpp +[ 28%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o +[ 28%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Compound.cpp.o +[ 31%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/Compound.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/Compound.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/Compound.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/Compound.cpp -[ 40%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o +[ 34%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o +[ 37%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o /usr/bin/c++ 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Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o -/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/Element.cpp -/usr/bin/c++ 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CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o -/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/Pdb.cpp -/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/TinkerAmber99.cpp -[ 53%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o -/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/VanderWallSphere.cpp -[ 56%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o -/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/VelocityRescalingThermostat.cpp -[ 59%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o -/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/VmdConnection.cpp In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ObcParameters.h:28, from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:50, from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:43: @@ -990,6 +1016,23 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 46%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o +/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/RiboseMobilizer.cpp +In file included from /build/reproducible-path/molmodel-3.1.0/src/AtomSubsystem.cpp:1: +/build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 180 | : public std::iterator > + | ^~~~~~~~ +In file included from /usr/include/c++/15/bits/stl_algobase.h:65, + from /usr/include/c++/15/bits/specfun.h:43, + from /usr/include/c++/15/cmath:3913, + from /usr/include/simbody/SimTKcommon/internal/common.h:255, + from /usr/include/simbody/SimTKcommon/basics.h:38, + from /usr/include/simbody/SimTKcommon.h:32, + from /usr/include/simbody/SimTKsimbody.h:43, + from /build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/AtomSubsystem.h:4: +/usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here + 129 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ObcParameters.h:28, from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:50, from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:40: @@ -1017,23 +1060,6 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/molmodel-3.1.0/src/AtomSubsystem.cpp:1: -/build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 180 | : public std::iterator > - | ^~~~~~~~ -In file included from /usr/include/c++/15/bits/stl_algobase.h:65, - from /usr/include/c++/15/bits/specfun.h:43, - from /usr/include/c++/15/cmath:3913, - from /usr/include/simbody/SimTKcommon/internal/common.h:255, - from /usr/include/simbody/SimTKcommon/basics.h:38, - from /usr/include/simbody/SimTKcommon.h:32, - from /usr/include/simbody/SimTKsimbody.h:43, - from /build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/AtomSubsystem.h:4: -/usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here - 129 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 62%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o -/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp In file included from /build/reproducible-path/molmodel-3.1.0/src/CompoundAtom.h:36, from /build/reproducible-path/molmodel-3.1.0/src/CompoundRep.h:42, from /build/reproducible-path/molmodel-3.1.0/src/CompoundSystem.cpp:3: @@ -1069,11 +1095,23 @@ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 50%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o +/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/TinkerAmber99.cpp +[ 53%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o +/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/VanderWallSphere.cpp +[ 56%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o +/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/VelocityRescalingThermostat.cpp +[ 59%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o +/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/VmdConnection.cpp +[ 62%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o +/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp [ 65%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/CpuObc.cpp [ 68%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.cpp [ 71%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.cpp.o +[ 75%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o +/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.cpp /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/ObcParameters.cpp In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp:25: /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1123,7 +1161,9 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.cpp:25: +[ 78%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o +/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.cpp +In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.cpp:25: /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ @@ -1144,15 +1184,7 @@ /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > { | ^~~~~~~~~~~~~~~ -/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 75%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o -/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.cpp -[ 78%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o -/usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.cpp -In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ObcParameters.h:28, - from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ObcParameters.cpp:26: +In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.cpp:25: /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ @@ -1176,6 +1208,9 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ [ 81%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp [ 84%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o @@ -1184,7 +1219,8 @@ /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/imd.cpp [ 90%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o /usr/bin/c++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=1 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"\" -DSimTKmolmodel_EXPORTS -I/build/reproducible-path/molmodel-3.1.0/src -I/build/reproducible-path/molmodel-3.1.0/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/vmdsock.cpp -In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.cpp:25: +In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ObcParameters.h:28, + from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ObcParameters.cpp:26: /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ @@ -1208,8 +1244,8 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.h:28, - from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.cpp:25: +In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.h:30, + from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:27: /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ @@ -1259,8 +1295,8 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.h:30, - from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:27: +In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.h:28, + from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.cpp:25: /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ @@ -1336,7 +1372,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/reproducible-path/molmodel-3.1.0/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/molmodel-3.1.0/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/molmodel-3.1.0 -B/build/reproducible-path/molmodel-3.1.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1415,11 +1451,11 @@ dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dpkg-shlibdeps: warning: symbol _ZN5gemmi12MaybeGzipped22uncompress_into_bufferEm used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol _ZN5gemmi12MaybeGzippedC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol _ZN5gemmi12MaybeGzippedD1Ev used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _ZN5gemmi12MaybeGzipped13create_streamEv used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _ZN5gemmi20read_pdb_from_streamERNS_9AnyStreamERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEENS_14PdbReadOptionsE used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _ZN5gemmi25make_structure_from_blockERKNS_3cif5BlockE used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol _ZN5gemmi12MaybeGzippedD1Ev used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol _ZN5gemmi12MaybeGzippedC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE used by debian/libsimtkmolmodel3.1t64/usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries dh_installdeb dh_gencontrol dh_md5sums @@ -1427,8 +1463,8 @@ dpkg-deb: building package 'libsimtkmolmodel-dev' in '../libsimtkmolmodel-dev_3.1.0-4.1_amd64.deb'. dpkg-deb: building package 'libsimtkmolmodel3.1t64' in '../libsimtkmolmodel3.1t64_3.1.0-4.1_amd64.deb'. dpkg-deb: building package 'libsimtkmolmodel3.1t64-dbgsym' in '../libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_amd64.deb'. -dpkg-deb: building package 'libsimtkmolmodel-plugins-dbgsym' in '../libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb'. dpkg-deb: building package 'libsimtkmolmodel-plugins' in '../libsimtkmolmodel-plugins_3.1.0-4.1_amd64.deb'. +dpkg-deb: building package 'libsimtkmolmodel-plugins-dbgsym' in '../libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../molmodel_3.1.0-4.1_amd64.buildinfo dpkg-genchanges --build=binary -O../molmodel_3.1.0-4.1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1436,12 +1472,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2133002/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2133002/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/219889 and its subdirectories -I: Current time: Thu Nov 19 08:19:47 -12 2026 -I: pbuilder-time-stamp: 1795119587 +I: removing directory /srv/workspace/pbuilder/2133002 and its subdirectories +I: Current time: Sat Oct 18 04:00:39 +14 2025 +I: pbuilder-time-stamp: 1760709639