Diff of the two buildlogs:
--
--- b1/build.log 2025-03-25 14:42:54.595945122 +0000
+++ b2/build.log 2025-03-25 14:46:29.418340179 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Tue Mar 25 02:39:27 -12 2025
-I: pbuilder-time-stamp: 1742913567
+I: Current time: Tue Apr 28 11:06:05 +14 2026
+I: pbuilder-time-stamp: 1777323965
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
@@ -28,54 +28,86 @@
dpkg-source: info: applying 968a0af8bc1a224337a3d1e1bd2fec3aec9e3fa1.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/46458/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/110547/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos6-i386.
+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 Apr 27 21:06 /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/110547/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/110547/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='i386'
- DEBIAN_FRONTEND='noninteractive'
- DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 '
- DISTRIBUTION='trixie'
- HOME='/root'
- HOST_ARCH='i386'
+ 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]="i686-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=i386
+ DEBIAN_FRONTEND=noninteractive
+ DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 '
+ DIRSTACK=()
+ DISTRIBUTION=trixie
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=i686
+ HOST_ARCH=i386
IFS='
'
- INVOCATION_ID='b8b5b97cc9d74608afd6a243fb047a88'
- LANG='C'
- LANGUAGE='en_US:en'
- LC_ALL='C'
- LD_LIBRARY_PATH='/usr/lib/libeatmydata'
- LD_PRELOAD='libeatmydata.so'
- 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='46458'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=30c3abef8b454735ba72275b6df863ee
+ LANG=C
+ LANGUAGE=de_CH:de
+ LC_ALL=C
+ LD_LIBRARY_PATH=/usr/lib/libeatmydata
+ LD_PRELOAD=libeatmydata.so
+ MACHTYPE=i686-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=110547
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.OvuxnTDo/pbuilderrc_81Bj --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OvuxnTDo/b1 --logfile b1/build.log molmodel_3.1.0-4.1.dsc'
- SUDO_GID='112'
- SUDO_UID='107'
- 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.OvuxnTDo/pbuilderrc_UR5e --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OvuxnTDo/b2 --logfile b2/build.log molmodel_3.1.0-4.1.dsc'
+ SUDO_GID=112
+ SUDO_UID=107
+ 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 ionos12-i386 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 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) 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/46458/tmp/hooks/D02_print_environment finished
+ lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/110547/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -268,7 +300,7 @@
Get: 139 http://deb.debian.org/debian trixie/main i386 libsimbody3.7 i386 3.7+dfsg-4 [3332 kB]
Get: 140 http://deb.debian.org/debian trixie/main i386 libsimbody-dev i386 3.7+dfsg-4 [2726 kB]
Get: 141 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
-Fetched 125 MB in 3s (48.3 MB/s)
+Fetched 125 MB in 4s (29.4 MB/s)
Preconfiguring packages ...
Selecting previously unselected package libproc2-0:i386.
(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 ... 19795 files and directories currently installed.)
@@ -855,7 +887,11 @@
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/110547/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for trixie
+I: user script /srv/workspace/pbuilder/110547/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
@@ -903,7 +939,7 @@
This warning is for project developers. Use -Wno-dev to suppress it.
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
--- Configuring done (1.4s)
+-- Configuring done (1.9s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
@@ -916,7 +952,7 @@
-- Build files have been written to: /build/reproducible-path/molmodel-3.1.0/obj-i686-linux-gnu
make[1]: Leaving directory '/build/reproducible-path/molmodel-3.1.0'
dh_auto_build
- cd obj-i686-linux-gnu && make -j11 "INSTALL=install --strip-program=true" VERBOSE=1
+ cd obj-i686-linux-gnu && make -j21 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/molmodel-3.1.0/obj-i686-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/molmodel-3.1.0 -B/build/reproducible-path/molmodel-3.1.0/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/molmodel-3.1.0/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/molmodel-3.1.0/obj-i686-linux-gnu//CMakeFiles/progress.marks
@@ -928,35 +964,51 @@
make[3]: Leaving directory '/build/reproducible-path/molmodel-3.1.0/obj-i686-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-i686-linux-gnu'
-[ 3%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/About.cpp.o
-[ 6%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o
-[ 9%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Biotype.cpp.o
-[ 12%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o
-[ 18%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o
-[ 18%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o
-[ 21%] 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 -Wformat -Werror=format-security -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
+[ 15%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Compound.cpp.o
+[ 15%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Biotype.cpp.o
+[ 15%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o
+[ 15%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o
+[ 15%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o
+[ 18%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystem.cpp.o
+[ 21%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PDBReader.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 -Wformat -Werror=format-security -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
-[ 25%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Compound.cpp.o
-[ 28%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystem.cpp.o
+[ 25%] 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 -Wformat -Werror=format-security -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
/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 -Wformat -Werror=format-security -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
+[ 28%] 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 -Wformat -Werror=format-security -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
/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/CompoundSystem.cpp
+[ 31%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o
+[ 34%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o
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-[ 31%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/MolecularMechanicsSystem.cpp
-[ 34%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PDBReader.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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/PDBReader.cpp
-[ 37%] 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 -Wformat -Werror=format-security -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
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[ 40%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.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 -Wformat -Werror=format-security -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
/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/PeriodicVmdReporter.cpp
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- from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:50,
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+/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 -Wformat -Werror=format-security -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
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+[ 59%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o
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+/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 -Wformat -Werror=format-security -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
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+/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 -Wformat -Werror=format-security -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
+[ 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 -Wformat -Werror=format-security -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
+/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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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
+In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/CpuObc.cpp:26:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
| ^~~~~~~~~~~~~~~
@@ -970,8 +1022,7 @@
from /usr/include/simbody/SimTKcommon/internal/common.h:257,
from /usr/include/simbody/SimTKcommon/basics.h:38,
from /usr/include/simbody/SimTKcommon.h:32,
- from /build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/common.h:40,
- from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:40:
+ from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
@@ -981,9 +1032,7 @@
/usr/include/c++/14/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/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:
+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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
| ^~~~~~~~~~~~~~~
@@ -997,8 +1046,7 @@
from /usr/include/simbody/SimTKcommon/internal/common.h:257,
from /usr/include/simbody/SimTKcommon/basics.h:38,
from /usr/include/simbody/SimTKcommon.h:32,
- from /build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/common.h:40,
- from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:38:
+ from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
@@ -1008,72 +1056,6 @@
/usr/include/c++/14/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<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
- 180 | : public std::iterator<std::forward_iterator_tag, std::pair<AtomSubsystem::AtomIndex, AtomSubsystem::AtomIndex> >
- | ^~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_algobase.h:65,
- from /usr/include/c++/14/bits/specfun.h:43,
- from /usr/include/c++/14/cmath:3906,
- 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
- 127 | struct _GLIBCXX17_DEPRECATED iterator
- | ^~~~~~~~
-[ 43%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/Representation.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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/Representation.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/Representation.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/Representation.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/Representation.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/Compound.cpp:45:
-/build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
- 180 | : public std::iterator<std::forward_iterator_tag, std::pair<AtomSubsystem::AtomIndex, AtomSubsystem::AtomIndex> >
- | ^~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_algobase.h:65,
- from /usr/include/c++/14/bits/specfun.h:43,
- from /usr/include/c++/14/cmath:3906,
- 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/src/Compound.cpp:32:
-/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
- 127 | struct _GLIBCXX17_DEPRECATED iterator
- | ^~~~~~~~
-In file included from /build/reproducible-path/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:
-/build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
- 180 | : public std::iterator<std::forward_iterator_tag, std::pair<AtomSubsystem::AtomIndex, AtomSubsystem::AtomIndex> >
- | ^~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_algobase.h:65,
- from /usr/include/c++/14/bits/specfun.h:43,
- from /usr/include/c++/14/cmath:3906,
- 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/CompoundSystem.h:4,
- from /build/reproducible-path/molmodel-3.1.0/src/CompoundSystem.cpp:1:
-/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
- 127 | struct _GLIBCXX17_DEPRECATED iterator
- | ^~~~~~~~
-[ 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 -Wformat -Werror=format-security -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
-[ 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
@@ -1098,9 +1080,19 @@
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
-[ 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 -Wformat -Werror=format-security -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
-In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/CpuObc.cpp:26:
+[ 71%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.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 -Wformat -Werror=format-security -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
+[ 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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
+[ 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 -Wformat -Werror=format-security -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
+/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/cpuObcInterface.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/DuMMForceFieldSubsystemRep.cpp:40:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
| ^~~~~~~~~~~~~~~
@@ -1114,7 +1106,8 @@
from /usr/include/simbody/SimTKcommon/internal/common.h:257,
from /usr/include/simbody/SimTKcommon/basics.h:38,
from /usr/include/simbody/SimTKcommon.h:32,
- from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28:
+ from /build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/common.h:40,
+ from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:38:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
@@ -1124,15 +1117,9 @@
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
-[ 71%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.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 -Wformat -Werror=format-security -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
-[ 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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
-[ 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 -Wformat -Werror=format-security -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
-In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.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/DuMMForceFieldSubsystemRep.h:50,
+ from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:43:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
| ^~~~~~~~~~~~~~~
@@ -1146,7 +1133,8 @@
from /usr/include/simbody/SimTKcommon/internal/common.h:257,
from /usr/include/simbody/SimTKcommon/basics.h:38,
from /usr/include/simbody/SimTKcommon.h:32,
- from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:28:
+ from /build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/common.h:40,
+ from /build/reproducible-path/molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:40:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
@@ -1156,8 +1144,26 @@
/usr/include/c++/14/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/ObcParameters.h:28,
- from /build/reproducible-path/molmodel-3.1.0/src/gbsa/ObcParameters.cpp:26:
+[ 87%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/imd.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 -Wformat -Werror=format-security -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
+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<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
+ 180 | : public std::iterator<std::forward_iterator_tag, std::pair<AtomSubsystem::AtomIndex, AtomSubsystem::AtomIndex> >
+ | ^~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_algobase.h:65,
+ from /usr/include/c++/14/bits/specfun.h:43,
+ from /usr/include/c++/14/cmath:3906,
+ 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
+ 127 | struct _GLIBCXX17_DEPRECATED iterator
+ | ^~~~~~~~
+[ 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 -Wformat -Werror=format-security -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:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
| ^~~~~~~~~~~~~~~
@@ -1181,9 +1187,8 @@
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
-[ 84%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o -c /build/reproducible-path/molmodel-3.1.0/src/gbsa/cpuObcInterface.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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
| ^~~~~~~~~~~~~~~
@@ -1207,10 +1212,6 @@
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
-[ 87%] Building CXX object CMakeFiles/SimTKmolmodel.dir/src/imd.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -1261,6 +1262,24 @@
/usr/include/c++/14/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/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:
+/build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
+ 180 | : public std::iterator<std::forward_iterator_tag, std::pair<AtomSubsystem::AtomIndex, AtomSubsystem::AtomIndex> >
+ | ^~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_algobase.h:65,
+ from /usr/include/c++/14/bits/specfun.h:43,
+ from /usr/include/c++/14/cmath:3906,
+ 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/CompoundSystem.h:4,
+ from /build/reproducible-path/molmodel-3.1.0/src/CompoundSystem.cpp:1:
+/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
+ 127 | struct _GLIBCXX17_DEPRECATED iterator
+ | ^~~~~~~~
In file included from /build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.h:28,
from /build/reproducible-path/molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp:27:
/build/reproducible-path/molmodel-3.1.0/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -1287,6 +1306,23 @@
/usr/include/c++/14/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/CompoundAtom.h:36,
+ from /build/reproducible-path/molmodel-3.1.0/src/CompoundRep.h:42,
+ from /build/reproducible-path/molmodel-3.1.0/src/Compound.cpp:45:
+/build/reproducible-path/molmodel-3.1.0/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
+ 180 | : public std::iterator<std::forward_iterator_tag, std::pair<AtomSubsystem::AtomIndex, AtomSubsystem::AtomIndex> >
+ | ^~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_algobase.h:65,
+ from /usr/include/c++/14/bits/specfun.h:43,
+ from /usr/include/c++/14/cmath:3906,
+ 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/src/Compound.cpp:32:
+/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
+ 127 | struct _GLIBCXX17_DEPRECATED iterator
+ | ^~~~~~~~
[ 93%] Linking CXX shared library libSimTKmolmodel.so
/usr/bin/cmake -E cmake_link_script CMakeFiles/SimTKmolmodel.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/molmodel-3.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--dependency-file=CMakeFiles/SimTKmolmodel.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libSimTKmolmodel.so.3.1 -o libSimTKmolmodel.so.3.1 CMakeFiles/SimTKmolmodel.dir/src/About.cpp.o CMakeFiles/SimTKmolmodel.dir/src/AtomSubsystem.cpp.o CMakeFiles/SimTKmolmodel.dir/src/Biotype.cpp.o CMakeFiles/SimTKmolmodel.dir/src/BondGeometry.cpp.o CMakeFiles/SimTKmolmodel.dir/src/Compound.cpp.o CMakeFiles/SimTKmolmodel.dir/src/CompoundSystem.cpp.o CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystem.cpp.o CMakeFiles/SimTKmolmodel.dir/src/DuMMForceFieldSubsystemRep.cpp.o CMakeFiles/SimTKmolmodel.dir/src/Element.cpp.o CMakeFiles/SimTKmolmodel.dir/src/MolecularMechanicsSystem.cpp.o CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o CMakeFiles/SimTKmolmodel.dir/src/Pdb.cpp.o CMakeFiles/SimTKmolmodel.dir/src/PeriodicVmdReporter.cpp.o CMakeFiles/SimTKmolmodel.dir/src/Representation.cpp.o CMakeFiles/SimTKmolmodel.dir/src/RiboseMobilizer.cpp.o CMakeFiles/SimTKmolmodel.dir/src/TinkerAmber99.cpp.o CMakeFiles/SimTKmolmodel.dir/src/VanderWallSphere.cpp.o CMakeFiles/SimTKmolmodel.dir/src/VelocityRescalingThermostat.cpp.o CMakeFiles/SimTKmolmodel.dir/src/VmdConnection.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuImplicitSolvent.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/CpuObc.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/ImplicitSolventParameters.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/ObcParameters.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMCommon.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMLog.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/SimTKOpenMMUtilities.cpp.o CMakeFiles/SimTKmolmodel.dir/src/gbsa/cpuObcInterface.cpp.o CMakeFiles/SimTKmolmodel.dir/src/imd.cpp.o CMakeFiles/SimTKmolmodel.dir/src/vmdsock.cpp.o /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/i386-linux-gnu/libz.so /usr/lib/i386-linux-gnu/libSimTKmath.so.3.7 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/liblapack.so /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm
@@ -1339,7 +1375,7 @@
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
- cd obj-i686-linux-gnu && make -j11 install DESTDIR=/build/reproducible-path/molmodel-3.1.0/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
+ cd obj-i686-linux-gnu && make -j21 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-i686-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/molmodel-3.1.0 -B/build/reproducible-path/molmodel-3.1.0/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
@@ -1417,25 +1453,25 @@
diversion by libc6 from: /lib/ld-linux.so.2
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux.so.2.usr-is-merged
-dpkg-shlibdeps: warning: symbol _ZN5gemmi12MaybeGzippedD1Ev used by debian/libsimtkmolmodel3.1t64/usr/lib/i386-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
-dpkg-shlibdeps: warning: symbol _ZN5gemmi8GzStream4getsEPci used by debian/libsimtkmolmodel3.1t64/usr/lib/i386-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
-dpkg-shlibdeps: warning: symbol _ZN5gemmi12MaybeGzipped22uncompress_into_bufferEj used by debian/libsimtkmolmodel3.1t64/usr/lib/i386-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
-dpkg-shlibdeps: warning: symbol _ZN5gemmi19remove_entity_typesERNS_9StructureE used by debian/libsimtkmolmodel3.1t64/usr/lib/i386-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/i386-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/i386-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
-dpkg-shlibdeps: warning: symbol _ZN5gemmi16assign_subchainsERNS_9StructureEbb used by debian/libsimtkmolmodel3.1t64/usr/lib/i386-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
+dpkg-shlibdeps: warning: symbol _ZN5gemmi12MaybeGzipped22uncompress_into_bufferEj used by debian/libsimtkmolmodel3.1t64/usr/lib/i386-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol _ZN5gemmi8GzStream4getcEv used by debian/libsimtkmolmodel3.1t64/usr/lib/i386-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
-dpkg-shlibdeps: warning: symbol _ZN5gemmi15change_ccd_codeERNS_9StructureERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_ used by debian/libsimtkmolmodel3.1t64/usr/lib/i386-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol _ZN5gemmi12MaybeGzipped24get_uncompressing_streamEv used by debian/libsimtkmolmodel3.1t64/usr/lib/i386-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
+dpkg-shlibdeps: warning: symbol _ZN5gemmi16assign_subchainsERNS_9StructureEbb used by debian/libsimtkmolmodel3.1t64/usr/lib/i386-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/i386-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
+dpkg-shlibdeps: warning: symbol _ZN5gemmi19remove_entity_typesERNS_9StructureE used by debian/libsimtkmolmodel3.1t64/usr/lib/i386-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
+dpkg-shlibdeps: warning: symbol _ZN5gemmi15change_ccd_codeERNS_9StructureERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_ used by debian/libsimtkmolmodel3.1t64/usr/lib/i386-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
+dpkg-shlibdeps: warning: symbol _ZN5gemmi12MaybeGzippedD1Ev used by debian/libsimtkmolmodel3.1t64/usr/lib/i386-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
+dpkg-shlibdeps: warning: symbol _ZN5gemmi8GzStream4getsEPci used by debian/libsimtkmolmodel3.1t64/usr/lib/i386-linux-gnu/libSimTKmolmodel.so.3.1 found in none of the libraries
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
-dpkg-deb: building package 'libsimtkmolmodel-plugins' in '../libsimtkmolmodel-plugins_3.1.0-4.1_i386.deb'.
-dpkg-deb: building package 'libsimtkmolmodel3.1t64-dbgsym' in '../libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_i386.deb'.
-dpkg-deb: building package 'libsimtkmolmodel-plugins-dbgsym' in '../libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_i386.deb'.
dpkg-deb: building package 'libsimtkmolmodel-dev' in '../libsimtkmolmodel-dev_3.1.0-4.1_i386.deb'.
+dpkg-deb: building package 'libsimtkmolmodel-plugins-dbgsym' in '../libsimtkmolmodel-plugins-dbgsym_3.1.0-4.1_i386.deb'.
dpkg-deb: building package 'libsimtkmolmodel3.1t64' in '../libsimtkmolmodel3.1t64_3.1.0-4.1_i386.deb'.
+dpkg-deb: building package 'libsimtkmolmodel-plugins' in '../libsimtkmolmodel-plugins_3.1.0-4.1_i386.deb'.
+dpkg-deb: building package 'libsimtkmolmodel3.1t64-dbgsym' in '../libsimtkmolmodel3.1t64-dbgsym_3.1.0-4.1_i386.deb'.
dpkg-genbuildinfo --build=binary -O../molmodel_3.1.0-4.1_i386.buildinfo
dpkg-genchanges --build=binary -O../molmodel_3.1.0-4.1_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
@@ -1443,12 +1479,14 @@
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/110547/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/110547/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/46458 and its subdirectories
-I: Current time: Tue Mar 25 02:42:53 -12 2025
-I: pbuilder-time-stamp: 1742913773
+I: removing directory /srv/workspace/pbuilder/110547 and its subdirectories
+I: Current time: Tue Apr 28 11:09:27 +14 2026
+I: pbuilder-time-stamp: 1777324167